Genetics Comprehensive Exam

Mediator

A protein complex that mediates between RNA pol II and the regulatory transcription factors

The nucleic acid genome of a virus may be

Circular or linear, DNA or RNA, double stranded or single stranded, a few thousand or more than 100,000 nucleotides

Bacterial chromosomes are

Circular, double stranded DNA and compacted into a nucleoid

Shell coiling in the water snail lymnaea is due to

Maternal effect inheritance

Tropomyosin plays a role in

Muscle contraction

HOX genes determine

The fate of each segment. Proteins activate the genes to make a specific body part. Trans acting

Linkage map

A genetic map based on the frequencies of recombination between markers during crossing over of homologous chromosomes

An individual with somatic cells that are genotypically different from each is called

A genetic mosaic

A gamete

A haploid reproductive cell

Genomic imprinting may involve

A single gene, a part of a chromosome, an entire chromosome, even all the chromosomes from one parent

Allele E1 encodes

An enzyme that functions better at lower temperatures

Double stranded RNA has a molecular signature associated with viruses

Can cause activation of anti-viral defense mechanisms

16S rRNA plays a key rold in codon-anticodon recognition

Can detect an incorrect tRNA bound at the A site. Prevents elongation until mispaired tRNA is released

DNA southern blots

Can detect the presence of a particular gene sequence within a mixture of many

Neutral mutation

Does not alter protein function

Silent mutations

Doesn't alter amino acids

Histone acetyltransferase

Enzymes which acetylate the positively charged lysines within the core histone proteins

Three types of dominant mutant alleles

Gain of function mutations, dominant negative mutations, haplo insufficiency

Studying regulatory elements traditionally uses enzymes

Galactosidase and glucuronidase

Recombinants

Gametes that carry a new combination of alleles

Sanger sequencing

DNA polymerase adds ddNTPS to the 3'OH end. There is no more 3'OH end so the reaction is cut off because there's no exposed O to attach more

CpG islands

DNA regions rich in C residues adjacent to G residues. Especially abundant in promoters, these regions are where methylation of cytosine usually occurs

DNA pol II, IV, V are involved in

DNA repair and replication of damaged DNA

Telomerase RNA functional role

DNA replication

3 classes of segmentation genes

Gap, pair rule, and segment polarity

Homologous recombination can lead to

Gene conversion

Mechanisms of gene redundancy

Gene duplication creates similar genes or paralogs. Genes may be involved in similar cell function

Gain of function mutations (dominant allele)

Gene gains a new or abnormal function. May be overexpressed, producing higher levels of the protein

Point mutation

Gene mutation in which a single base pair in DNA has been changed

X-chromsome ianctivation

In each cell of the earl embryo, one X chromosome becomes a Barr body

Operons involved in catabolism are typically

Inducible. The substance to be broken down acts as the indcuer

Likely effect on protein function in frameshift mutation

Inhibitory

Likely effect on protein function in nonsense mutation

Inhibitory

Translation can be viewed as occuring in three stages

Initiation, elongation, and termination

Copia elements demonstrate regulatory effects at the point of

Insertion in the chromosome

Biological significance of imprinting

Not well understood

Alignment identifies

Overlapping sequences, allowing reconstruction of their order in a chromosome

Minor contamination of sample DNA can cause major problems in

PCR

Deamination

Removal of an amino group from cytosine base resulting in uracil. May be corrected, may result in deaminate 5 methyl cytosine resulting in thymine (hot spot for mutation)

Alloploidy

Polyploid organism that contains the genomes of two or more different species. Interspecies cross

Deletion

Portion of chromosome is missing

Duplication

Portion of chromosome is repeated

Chromosome structure alteration: duplication

Portion of the chromosome is repeated

Coupling RT with PCR

Semiquantitative allows user to compare expression of genes between two samples

Simple mendelian inheritance describes inheritance patterns that obey

The law of segregation and the law of independent assortment

Insertion of P elements into the promoter can affect

The level of gene expression

The 23S rRNA is the component of the 50S subunit that acts as

The peptidyl transferase

mRNA transcription terminates when the 3' end dissociates after

The poly-A signal sequence

I on the lac operon is

Trans acting

ncRNA molecules involved with translation

tRNA, rRNA, antisense RNA

Codons are recognices by the anticodon of

tRNAs

The 3D structure of release factors mimics

tRNAs

ncRNAs and miRNA processing components may be effective targets for novel treatment therapies

Therapies that inhibit miRNA function or therapies that restore miRNA function

Steroid hormones are lipids

They can pass through plasma membrane

Sex limited traits

Traits that occur in only one of the two sexes. Responsible for sexual dimorphism. May be autosomal or sex linked

The action of the lac repressor on the lac operon is a

Trans acting factor

RNA polymerase II in eukaryote transcription

Transcribes all proetin encoding genes. Responsible for the synthesis of all mRNAs

RNA pol II

Transcribes all protein encoding genes, thus synthesizes all mRNAs. Transcribes some snRNA genes

RNA polymerase II in transcription

Transcribes protein encoding genes

Negative regulation: no repressor

Transcription

No proofreading in

Transcription

There is rho independent and rho dependent termination in

Transcription

The biological advantage of alternatice splicing is that

Two or more polypeptides can be derived from a single gene

RNA northern blotting

Used to identify specific RNAs within a mixture of many RNA molecules. Similar to DNA blotting

Spreading in X inactivation

Xist expressed on chromosome to be inactivated, Xist transcripts coat chromosome, proteins recruited to chromosome to condense it

Different species can be distinguished from each other based on the number and size of

Chromosomes

Genomic library

Composed of chromosomal DNA fragments. Should represent all of the DNA of the cell

Promoter in bacteria

Consists of -35 and -10 sequences

Unregulated gene expression

Constitutive (constant). Essentially constant levels of expression. Frequently for proteins that are continuously necessary for the survival of the organism

Cetromere

Constricted region of the chromosome, which has a role in chromosome segregation during mitosis and meiosis

miR-1 is associated with the development of

Heart arrhythmias (irregularities in the rate or rhythm of the heartbeat). Regulates expression of genes that encode ion channel proteins, which are important for proper signaling between cardiac muscle cells

Variable characteristics of pea plants

Height, flower color, flower position, seed color and shape, pod color and shape

Keto tautomeric shift

Enol form (lose H) T and G

Occasionally, whether a mutation is beneficial or deleterious will depend on

Environmental conditions

What determines exit from latency?

Environmental conditions

The epigenome is cell type specific and changes throughout the life cycle in response to

Environmental cues

Maternal imprinted

Father's allele is expressed

Transmission patterns for X linked genes

Fathers transmit X only to daughters, and sons receive their X only from their mothers

Control of protein function in posttranslational regulation can occur by

Feedback inhibition or covalent modification of amino acids in the protein

Homogametic sex

Female that is X-X. All eggs carry X plus 22 autosomes

Alloploidy plants may undergo nondisjunction and produce

Fertile offspring

Nuclear lamina

Fibers lining the inner membrane

Mechanism of RNAi

First pri-miRNA is made which forms a hairpin. Cleaved to 70 nucleotide pre-miRNA and exported from the nucleus to the cytoplasm where it's cut by DICER to 20-25bp

Initiation in eukaryotes

Five general transcription factors assemble at the core promoter

Simple transposons

Flanking direct repeats, inverted repeats, transposase gene. Carry one or more genes not necessary for transposition

Key enzymes

Histone acetyltranferase/histone deacetylase. Histone methyltransferase/histone demethylase

HOTAIR is transcribed from the opposite (antisense) strand with respect to the

HoxC genes

Each chromosome carries

Hundreds of thousands of different genes

Types of product that comes out of a DNA ligation

Insert DNA ligated to itself, empty plasmid, plasmid with an insert

Insertions and deletions in coding regions for proteins can

Insert new amino acids or cause a shift in the reading frame

mRNAs have different

Molecular weights

When morgan studied flies and found X linked traits

Mostly combinations of traits like the parents meaning that all three genes observed are located on the X chromosome and transmitted together as a unit

In myotonic muscular dystrophy, the TRNE is more likely to occur if inherited from the

Mother

Genetic material replication

Must be copied to be passed from parent to offspring

Some genes do not encode polypeptides but are transcribed into

Non coding RNAs (ncRNAs)

Nonhomologous end joining

Occrus at the double strand breaks. The broken ends are recognized by proteins that keep the ends together; the broken ends are eventually rejoined

Some human aneuploidies are influenced by parental age

Older parents more likely to produce abnormal offspring

Specific pattern of splicing involved proteins known as

Splicing factors. Play a key role in determining splice sites

Homologous recombination repair

Strand of normal sister chromatid is used to repair damaged sister chromatid

The length of telomeres is maintained using the enzyme

Telomerase

In the formation of haploid cells

Chromosomes segregate independently

Human mitochondrial diseases are typically

Chronic degenerative disorders affecting cells that need high levels of ATP: nerve and muscle cells

P and O are components of the lac operon that are

Cis acting

Lac operator is a

Cis acting element

Factors that control gene expression can be divided into two types based on their location

Cis acting elements and trans acting factors

Restriction enzymes bind to specific DNA sequences and

Cleave the phosphodiester backbone of the DNA at defined locations on each strand

cDNA pros and cons

Clone abundance equals the percent of mRNA transcript in starting tissue. No introns or promoters. Less junk

DNA amplification used to study DNA

Cloning vectors-DNA replication in cells and amplification in vitro-thermostable DNA polymerases

Plasmid

A small ring of DNA that carries accessory genes separate from those of the bacterial chromosome

Oligonucleotide with reporter at one end, quencher at the other

Complementary to the PCR product

Chromosome structure alteration: deletion

AKA deficiency. Portion of chromosome is missing

Adaptation of CRISPR defense

AKA spacer acquisition. Cas1 and 2 protein complex cleaves bacteriophage DNA and a piece of this is inserted into the spacer region of the Crispr gene

Deletion/insertion

Addition or removal of bases

The first amino acid in a polypeptide chain has an exposed

Amino group; N-terminus or amino terminal end

Tn elements

Can introduce multi-drug resistance onto bacterial plasmids (R factors)

Isoacceptor tRNAs

Can recognize the same codon

In both plants and animals, the action of transcription factors depends on

Changes in chromatin structure, making genes available for expression

Aneuploidy

Changes in chromosome nu,ber

qPCR uses a thermocycler that can measure

Changes in fluorescence from detector molecules

Transcriptional activation in eukaryotes involves

Changes in nucleosome locations, nucleosome composition, and histone modifications

What affects the degree of chromatin compaction during the life cycle of the cell?

Changes in the proteins

Mutagenic agents are usually classified as

Chemical or physical mutagens

Histone modification alter

Chromatin conformation and protein interactions with the DNA strand

Plasmids exist independently of

Chromosomal DNA

Three alleles affect the sugar addition in ABO blood type genes

i allele, IA, IB

Presence of the Xist transcript on the Xi chromosome results in the recruitment of

macroH2A

Nonpolar amino acids are hydrophobic

They are often buried within the interior of folded protein

Linked assortment

Variants found together in parents are always inherited as a unit

eIF

Eukaryotic initiation factors

Evo-devo

A field that combines evolutionary and developmental biology

Haplodiploid sex determination is found in

Bees, wasps, and ants

Coupling RT with qPCR

Can numerically estimate the difference in expression

Causes of mutations

Can occur spontaneously or be induced

The 7-methylguanoisine cap structure is recognized by

Cap binding proteins

RNA interference is transcribed from

Endogenous eukaryotic genes

RNA interference is a major mechanism of

Gene expression regulation in eukaryotes

By the end of prophase, sister chromatids are entirely

Heterochromatic

Chromatin can be 2 forms

Heterochromatin or euchromatin

Base pairs per turn of the helix

10

TFIID

A general transcription factor that recruits RNA pol to the promoter

Gene sry

A single gene on the Y chromosome that is responsible for male development

Alleles

Different versions of the same gene

Homeotic selector

Hox genes specify the fate of each segment

Different types of transposable elements have

Characteristic DNA sequences

Beta clamps

Keeps pol III attached to DNA

Character

Characteristics that can vary such as height

Germ line mutation

Mutation that can be passed onto offspring

Template DNA in PCR

Contains the region that needs to be amplified

Allosteric enzyme

Contains two different binding sites

In huntington's disease, the TRNE is more likely to occur if inherited from the

Father

Examples of nucleotides

AMP, ATP, ADP

The predominant form of double helix found in living cells

B DNA

Inhibitors

Bind activators and prevent them from binding to DNA

Denaturation in PCR

DNA strands separated

lacZ gene

Encodes beta-galactosidase

Pair rule mutations

Every other segment deleted

Smaller things move through thick substances

Faster than larger things

Mutation most likely to cause phenotype

Frameshift mutation

Mutagens are often involved in the development of

Human cancers

DNA ligase

Joinds fragments together

Capsid

Outer protein coat of a virus

Original DNA strands

Parental strands

Chaperones

Proteins that help folding

The ribosome is a ribozyme

RNA acts as an enzyme

Telomere sequence for humans

TTAGGG

tRNAs are named according to

The amino acid they bear

The nuclear matrix organizes

The chromosomes within the nucleus

Wild type

The relatively prevalent genotype

Blotting uses a probe

To visualize

RF1 recognizes

UAA and UAG

If ncRNAs are expressed abnormally

Disease conditions can occur

When exposed to both lactose and glucose

E. coli uses glucose first, and catabolte repression prevents the use of lactose. When glucose is depleted, catabolite repression is alleviated and the lac operon is expressed

TFIID

A complec of proteins that includes the TATA binding protein (TBP) and several TBP associated factors

Trisomy

A condition in which an extra copy of a chromosome is present in the cell nuclei, causing developmental abnormalities

The homeodomain

A conserved sequence of 60 amino acids used in the binding to DNA. Usually found in transcription factors, it is used to express genes that are related, more specifically in development to make tissues associated with one another.

Barr body

A dense body formed from a deactivated X chromosome.

Nucleosomes associate with each other to form

A more compact structure 30nm fiber

In deamination, if repair system fails to correct the problem

A mutation could result during subsequent round of DNA replication

Apurinic sites can be repaired, but if the repair system fails

A mutation may result

Somatic mutation

A mutation that cannot be passed onto the offspring

Neutral mutation

A mutation that has no effect on the organism. Does not alter protein function

ncRNA scaffold

A ncRNA binds a group of proteins

ncRNA guide

A ncRNA binds to a protein and guides it to a specific site in the cell

Alteration of protein function or stability by ncRNA

A ncRNA can bind to a protein and alter the proteins structure, ability of the protein to act as a catalyst, to bind to another molecule, change protein stability

Genes that play a role in disease may exist as

A normal allele or a mutant allele that causes disease symptoms

A gene is called recessive if the heterozygote has

A normal phenotype. One wild type copy is sufficient to provide full function

The chromosome theory of inheritance confirmed that

A particular gene was localized to a chromosome

Conjugation bridge

A passageway for the transfer of the genetic information from the F+ to the F-

Nucleotides are covalently linked by

A phosphodiester bond

Relaxosome

A protein complex that recognizes the origin of transfer in F factors and other conjugative plasmids, cuts one DNA strand, and aids in the transfer of the T DNA

Base analogs

A purine or pyrimidine that differs in chemical structure from those normally found in DNA or RNA. Can substitute for purines or pyrimidines during nucleic acid replication

A transversion is a change of

A pyrimidine to a purine or vice versa

Mechanism of counting X chromosomes in cells relies on

A region of the X chromosome called the X inactivation center (Xic)

Repressor

A regulatory protein that binds to the DNA and inhibits transcription

Activator

A regulatory protein that increases the rate of transcription

An operon

A regulatory unit consisting of a few structural genes under the control of one promoter

The number of recombinants are used to calculate

A relative distance between the genes

The core promoter

A relatively short DNA sequence that is necessary for transcription to take place. Consists of TATA box and the transcriptional start site

Allopolyploids can mutate again to regain fertility

A second defective cell division can turn them into fertile polyploids which produce diploid gametes

Suppressor mutations

A second mutation that affects phenotypic expression of the first mutation

Suppressor

A secondary mutation that can cancel the effect of a primary mutation, resulting in a wild-type phenotype. Different than a reversion-occurs at a second site

Polymerase chain reaction

A way to make many copies of a particular DNA sequence

5' and 3' UTR

Affects stability of RNA and/or translation

Mutations generate

Allelic variations

RNaseMRP

An RNA protein complex involved in processing some rRNAs, mRNAs, and mitochondrial RNAs

Autosomes

Any chromosome that is not a sex chromosome

Formation of RNA flaps

DNA pol delta elongates an okazaki fragment until it runs into the RNA primer of the adjacent fragment, causing the RNA to form a small flap

Cis-acting elements

DNA sequences in the vicinity of the structural portion of a gene that are required for gene expression. On the same DNA strand that allows binding of transcription factors

Cis regulatory elements

DNA sequences on the same DNA strand as the gene they regulate

Small RNAs in prokaryotes

CRISPR

Photolyase in direct repair

Can repair thymine dimers. Splits the dimers, restoring the DNA to original condition. Uses light called photoreactivation

Insertion of P elements into the coding region of a gene

Can terminate transcription destroying normal gene expression

Auxotrophs

Cannot synthesize a needed nutrient

mRNA modification

Capped, spliced, polyadenylated

Each capsid is made of identical protein subunits called

Capsomers

Last amino acid on a polypeptide chain has an exposed

Carboxyl group: C-terminus or carboxy terminal end

Inside to outside of flower

Carpel, stamen, petal, sepal

MADS box floral homeotic transcription factor genes (A, B, C) control the development of

Carpel, stamen, petal, sepal

The initiator tRNA is designated tRNA met

Carries a methionine rather tna a formylmethionine

tRNA involved in protein synthesis

Carry amino acids

Peptidyl transferase

Catalyzes the peptidyl transfer reaction. Where the polypeptide in the P site is transferred to the amino acid at the A site, forming a peptide bond

Viral reproduction uses reverse transcriptase to

Copy RNA into DNA for integration. Once integrated, the genome is called a provirus

Attenuation occurs in bacteria because of

Coupling of transcription and translation

DNA ligase

Covalently links the DNA backbones

Base modifiers

Covalently modify nucleotide structure

Base modifiers

Covalently modify nucleotide structure. Ex: nitrous acid replaces amino groups with keto groups

Parts of the operon

Promoter, CAP site, operator, protein coding genes, terminator

All three splicing mechanisms involve

Removal of intron RNA and linkage of the exon RNAs by a phosphodiester bond

RNA polymerase moves along the template strand in a 3' to 5' direction

RNAis synthesized in a 5' to 3' direction

DICER

Recognized double stranded RNA and cuts in into short double stranded pieces

Nucleotide excision repair

Recognizes DNA damage and remove several to many nucleotides

Filters are placed into a buffered solution containing a primary antibody

Recognizes the protein of interest but usually lacks a label

The tRNAs play a direct role in recognition of codons in mRNA

Recognizing a 3base codon in mRNA and carrying an amino acid that is specific for that codon

Genes regulated by small effector molecules that inhibit transcription are called

Repressible genes

Operons involved in anabolism are typically

Repressible. The inhibitor or corerpressor is the small molecule that is the product of the operon

trp repressor protein

Repression is achieved when the amino acid tryptophan binds to the repressor protein. The complex then binds the operator region to block transcription

Regulatory protein that decrease the rate of transcription are termed

Repressor sequences and they bind to silencer elements

Corepressors bind to

Repressors and cause them to bind to DNA

Activator proteins enhance the function of TFIID

Recruit TFIID to the TATA box or help it recruit RNA pol II, or interact with coactivators that act on TFIID

Activator proteins: aid TFIID

Recruitment to TATA box. Aids in recruiting RNA polymerase. Interact with coactivators

Silencers

Reduce transcription

Outcome of a HOTAIR ncRNA that could no longer binds to PRC2

Reduced methylation of H3K27 and possible upregulation of transcription of target genes

Enzymes are only one category of proteins

Some genes encode other types of proteins

rRNA modification

Spacer regions removed to produce 3 functional fragments

The degree of splicing and alternative splicing varies greatly among

Species

Zygotic genes: Homeotic selector (HOX) genes

Specify the fate of each segment

A single bacterial cell usually takes up a single copy of

The hybrid vector

Studying regulatory elements now usually fluorescent proteins

Either on their own or as fusion proteins

Proteins can be transferred from gels to membrane by

Electrophoresis

Col plasmids

Encode colicins, proteins that kill other bacteria

Main function of genetic material is to

Encode for the production of cellular ptoeins

IA alleles in ABO blood type

Encodes a form of the enzyme that can add the sugar N-acetylgalactosamine to the carbohydrate tree (makes A anitgen)

IB alleles in ABO blood type

Encodes a form of the enzyme that can add the sugar galactose to the carbohydrate tree (makes B atigen)

trpL

Encodes a short peptide termed the leader peptide

lacY

Encodes lactose permease. Membrane protein required for transport of lactose and analogues into the cell

lacA

Encodes transacetylsae. Covalently modifies lactose and analogues. Its functional necessity remains unclear

Steroid hormones are produced by

Endocrine glands

Diploid animals sometimes produce tissues that are polyploid

Endopolyploidy. Liver cells can be triploid, tetraploud, or even octaploid

TFIID and TFIIB recognize promoter region in

Eukaryotes

The recessive trait disappears entirely in the

F1 but reappears unchanged in the F2

Primase

Synthesizes the RNA primers

Genetic variation results from changes at

The molecular level

Meiotic non disjunction

Failure of chromosomes to segregate properly in anaphase. Can occur in meiosis I or II. Can produce cells with too many or few chromosomes and creates zygotes with abnormal chromosome numbers.

In eukaryotes RNA primers are removed by

Flap endonuclease

Intercalating agents contain

Flat planar structure that intercalate into the double helix

Most mitichondrial proteins are encoded by genes in

The nucleus. Proteins are made in the cytoplasm but have signal to direct them to

Eukaryotic replication begins with assembly of

The pre-replication complex (preRC)

Linkage refers to

Genes that are generally transmitted together

MutL, MutH, and MutS

Genes that detect mismatch and direct its removal from the newly made strand

Two categories of genes are associated with ncRNAs and neurological disorders

Genes that encode miRNAs and genes that encode proteins involved in processing miRNAs

Trans acting factors mediated by

Genes that encode regulatory proteins

Sex linked genes

Genes unique to X or Y

Multiple alleles

Genes with three or more alleles rather than the standard two. Exhibit codominance (both alleles are expressed)

Deleterious mutation

Genetic changes that are harmful to an organism. Lowers the chance of survival and reproduction. Good for studying genetics

Trans effect or trans acting factor

Genetic regulation that can occur even though DNA segments are not physically adjacent

Suppressor can be reversion in phenotype but not

Genetically because it's happening in a second gene

An epitote

Has a 3D structure that an antibody recognizes

Temperate phage

Has both latent and lysogenic cycles

Virulent phage

Has only a lytic cycle. Not capable of integration into the genome

Homologous genes are best described as genes that

Have a common ancestral gene

Libraries aim to

Have clones of all pieces of DNA in a genome (genomic library) or expressed in a tissue (cDNA library)

Polymorphism

In large populations, there may be more than one common allele considered to be wild type. This is known as genetic polymorphism

Pre-mRNA can be spliced

In more than one way

Reciprocal translocations are usually without phenotypic consequences

In some cases they can result in position effect

The RNA transcript is synthesized during the elongation step

In the 5' to 3' direction. Phosphodiester bonds are formed between the ribonucleotides

Monoallelic expression

In the case of imprinting, refers to the phenomenon that only one of the two alleles of a given gene is transcriptionally expressed

Artificial transformation

In transformation when DNA uptake occurs with the help of special techniques

ddNTPs

Lack a hydroxyl group

Inheritance patterns that deviate from Mendels law are seen when one allele is

Lethal

Semi lethal alleles

Lethal in some

Structure and number of chromosomes are typically studied by

Light microscopy

Some areas of the chromosome have a lower change of crossing over

Like near the centromere

Mutation rate

Likelihood that a gene will be altered by a mutation

Mutation rate

Likelihood that a gene will be altered by a mutation. Commonly expressed as the number of new mutations in a given gene/cell generation

Deleterious mutation

Lowers chance of survival and reproduction

Three natural mechanisms by which the chromosome number of a species can vary

Meiotic nondisjunction, mitotic nondisjunction, allploidy (interspecies crosses)

3 classes of cellular RNAs directly involved in protein synthesis

Messenger RNA, ribosomal RNA, transfer RNA

Chromatin structure is modified through

MethylCpG-binding protein which recruits other proteins, such as histone deacetylase, that modify the chromatin leading to a closed conformation

DNA methylation is heritable

Methylated DNA sequences are inherited during cell division

At least some genes are silenced on inactive X chromosomes by

Methylation

Genomic imprinting must involve a marking process that is reversible

Methylation of DNA bases

Maintenance methylation

Methylation pattern is maintained in the resulting offspring. Hemimethylated DNA is recognized by DNA methyltransferase, which makes it fully methylated

Karyotype

Microgrpah of all chromosomes in a cell (metaphase)

Endosymbiosis theory

Mitochondria and chloroplasts originated from bacteria that took up residence within a primordial eukaryotic cell

Paternal leakage

Mitochondria inherited from father via sperm

Species with maternal inheritance may, on occasion, exhibit paternal leakage

Mitochondria provided through the sperm

Heteroplasmy

Mix of wild type and mutant chloroplast or mitochondria in one cell

Second step of gene cloning

Mix the chromosomal DNA fragments with the digested vector and add DNA ligase to join them together

Transposable elements

Mobile pieces of DNA that can copy themselves into entirely new areas of the chromosomes. Can move around the genome

DNA methylation

Modifications to DNA elements or to their accessibility

In plants, sterile hybrids may be

More vigorous than the parent species and propagate asexually

Twin spot

Mosaic arising from mitotic recombination

Polyploidy can be induced by abrupt temperature changes or drugs

Most commonly the drug colchicine is used. Binds and stabilizes tubulin (a protein found in the spindle apparatus), promoting nondisjunction

Homeotic genes are activated as

Targets of the segmentation genes and determine the adult structures formed by each segment

Environmental agents can affect epigenetic regulation

Temperature, diet, toxins

A codon is always shown as the sense strand

Template DNA strand is antisense

Starting material for PCR

Template DNA, oligonucleotide primers, deoxynucleoside triphosphates (dNTPs), thermostable DNA polymerase

Tautomeric shift

Temporary change in base structure that promotoe A-C and G-T base pairing

Tautomeric shifts

Temporary change in base structure. Rare forms promote A-C and G-T base pairs that cause a mutation if it occurs immediately prior to replication

Aerobic organisms use oxygen as

Terminal electron acceptor

Stop codons

Termination or nonsense codons. (UAA, UAG, UGA)

Sex linked traits can be confirmed by

Test crosses

Synthesis of the leading strand is continuous and

That of the lagging strand is dicontinuous

A phosphate connects the 5' carbon of one nucleotide to

The 3' carbon of another nucleotide

mRNA transcription terminates when

The 3' end is cut just past the polyA signal sequence

Destabilizing elements are most common at

The 3' unsaturated region (3' UTR). The 3' end between the stop codon and the polyA tail

Polypeptide synthesis has a directionality that parallels

The 5' to 3' orientation of mRNA

A site in prokaryotic chromosome called the CRISPR locus regulates

The CRISPR-Cas system in bacteria. Contains segments that are derived from bacteriophage DNA

Primary structue of a protein

The amino acid sequence. The amino acids each have a unique side chain or R group

Leader peptide has several codons for

The amino acid whose biosynthesis is the result of the expression of the operon. If enough of the amino acid is still present, rest of operon is not expressed

Elongation in translation

The amino acids are added to the polypeptide chain, one at a time

A nucleotide deletion in DNA replication causes

The amino acids downstream from the deletion to be incorrect

Action of the maternal and segmentation genes defines

The anterior-posterior axis which is the field of action of the homeotic genes

SRP RNA provides a scaffold for

The binding of SRP proteins

Combinatorial control of transcription factors refers to the phenomenon that

The combination of many factors determines the expression of any given gene

Evolutionary mechanisms for differential development or organisms include

Mutation, gene duplication and subsequent divergence, assignment of new functions to old genes, recruitment of genes to new developmental pathways

Insertion of transposons can cause

Mutations

Several inherited limb malformations are caused by

Mutations in HOXD genes

Estimated that 1/3 of all genes are essential (required for survival)

Mutations in these genes can form lethal alleles

Random mutation theory

Mutations occur in any gene or piece of DNA randomly (although there may be hot spots). Do not need selection for mutation to occur. Growth condition may then select for most adapted organism

Start codon is AUG in some cases GUG or UUG but the first amino acid is always

N-formylmethionine

Two steps of transormation

Natural transformation and artificial transformation

Reverse transcriptase

Naturally occurring enzyme in retroviruses to copy their RNA genome to DNA

Mendel's Law of Segregation

The two copies of a gene segregate (or seperate) from each other during transmission from parent to offspring

ATs are easier to separate because of

The two hydrogen bonds instead of three

In the replisome, two DNA pol III proteins act in concert to replicate both the leading and lagging strands

The two proteins form a dimeric DNA polymerase that moves as a unit toward the replication fork

A strategy that inhibits miRNA function for treating certain cancers

The use of anti-miRNA oligonucleotides (AMOs)

When allolactose is available it binds to the repressor

This alters the conformation of the repressor protein, which prevents it from binding to the operator site. Therefore, RNA polymerase can transcribe the operon

Depending on whether a purine or phyrimidine is removed in base excision repair

This creates an apurine and apyrimidine site respectively

Nonionizing radiation

UV. Thymine dimers (crosslinked Ts)

In simple translocations the transfer of genetic material occurs in only one direction. AKA

Unbalanced translocations

Ames test

Used to determine if something is a mutagen

Recombinant analysis example

WWBB x wwbb then WwBb x wwbb

Hybridization

When plants with different traits are crossed. The result are called hybrids

Coupling between transcription and translation

When translation begins before transcription ends

Why the percentage of recombinant offspring plateaus at 50%

When two different genes are more than 50 map units apart, they follow the law of independent assortment in a testcross

DNA sequence alignments

Where similar sequences of bases are lined up for comparison

The stability of mRNA can be regulated so that its half life is shortened or lengthened

Will greatly influence the mRNA concentration and consequently gene expression

Most response elements are located

Within 200bp upstream of the promoter, but some are found at other various sites

Triple X syndrome

XXX two Barr bodies

Klinefelter syndrome

XXY one Barr body

The diploid cell from complete nondisjunction can participate in fertilization with a normal gamete

Yielding a triploid individual

The genetic material in chloroplasts

cpDNA

In eukaryotes one release factor recognizes all three stop codons

eRF1. eRF3 is also needed for termination

Therapies that restore miRNA function are needed for

miRNAs that behave like tumor suppressors

RNA interference is mediated by

microRNAs or small interfering RNAs

Crossing over produces

recombinant chromosomes, which combine DNA inherited from each parent

RNA modification

tRNA, rRNA, and mRNA are all modified

Reject null hypothesis if p value is

0.05 or less

DNA polymerases go in the direction of

5' to 3'. It requires a nucleotide primer with a free 3' -OH

DNA polymerase I

5' to 3'. Primarily acts on only the lagging strand to remove RNA primers from okazaki fragments. Uses 5'-3' polymerase activity to replace RNA with DNA

Alterations in chromosome number frequently occur during gamete formation

5-10% of embryos have an abnormal chromosome number. 50% of spontaneous abortions are due to such abnormalities

Together the nucleosomes and fiber shorten the DNA

50 fold

Amount of transposable elements in the human genome

50%

Why one wild type copy is sufficient to provide full function

50% of normal levels of protein are good enough. The one wild type copy is up regulated in expression, to produce adequate amount of functional protein

Standard gel electrophoresis can separate DNA up to

50kb. Can adjust agarose concentrations for different sizes

Origin recognition complex

6 proteins. Acts as initiator of DNA replication

ER signal sequences

6-12 amino acids. Hydrophobic and near the N terminus

Number of codons

64

In a typical human cell, only about 20% of transcription involves the production of mRNAs whereas

80% of it is associated with making ncRNAs. Ribosomal RNAs and transfer RNAs are a large part of that

Long non coding RNAs (lncRNAs)

>200 nucleotides

Inheritance patterns that deviate from Mendels law are seen when the alleles don't have

A simple dominant/recessive relationship

RNA polymerase in bacteria

A single RNA polymerase

A point mutation

A single base pair change

Gene libraries can be made from subgenomic fractions such as

A single chromosome generated by methods such as flow sorting and pulsed field gel electrophoresis

Like chloroplasts, mitochondria contain

A single circular chromosome. Contained within the nucleoid. Multiple copies of the single chromosome

The chromosome of both mitochondria and chloroplasts is composed of

A single circular double stranded DNA

Only tryptophan and methionine are encoded by

A single codon

One gene one enzyme hypothesis

A single gene controlled the synthesis of a single enzyme

Most genes can be pleiotropic

A single gene determines more than one phenotype for an organism

Polycistronic mRNA

A single molecule of messenger RNA that is formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA

Viral and bacterial chromosomes

A single nucleic acid molecule, few if any associated proteins, much smaller than eukaryotic chromosomes

Apurinic site

A site in DNA that is missing a purine base

Incomplete penetrance

A situation in which an allele is expected to cause a particular phenotype, but does not in a given individual. An individual who carries a dominate allele does not show the phenotype of that allele

Inducer

A small effector molecule that causes transcription to increase

Switch from active to inactive relies on

A small molecule

Segmental duplication

A small segment of a chromosome that has a tandem duplication

Pre-mRNA introns are removed via

A splicesome

Fluorescence amounts can be compared to

A standard of known amounts of template. Different colored fluorescent molecules distinguish the test product from the standard

Intergenic suppressor

A suppressor mutation that is in a different gene from the gene that contains the first mutation. Second mutation is in a different gene than the first

In early stages of embryo development, the zygote nucleus undergoes a number of divisions without cytokines and creates

A syncytium

Genetic mapping experiments are accomplished by carrying out

A testcross

Endosymbiosis

A theorized process in which early eukaryotic cells were formed from simpler prokaryotes

In meiosis I, homologous chromosomes synapse with each other. For normal and inversion chromosomes to synapse properly

An inversion loop must form

Segregation analysis is used to follow the inheritance of traits relative to each other

Can map relative to how frequently recombination occurs between them

TEs influence on mutation and evolution

Can rapidly enter genome and proliferate. Can be a major part of genomes

Competent cells

Are able to take up naked DNA. Cells that can be transformed by extracellular DNA

tRNA modification

Are processed by exonucleases (cut at the end of a strand) and endoculeases (cut within a strand)

Centromere

Area where the chromatids of a chromosome are attached

Emerging viruses

Arose recently and are more likely to cause infection than previous strains

Active genes in eukaryotes have a nucleosome free region

Around the core promoter and the termination site

Helix is right handed

As is spirals away from you, the helix turns in a clockwise direction

RT-PCR can detect expression of small amounts of RNA in a single cell and is semi quantitative

As long as cycle number is restricted

During bacterial translation, the mRNA lies on the surface of the 30S subunit

As polypeptide is being synthesized, it exits through a hole in the 50S subunit

Multiple crossovers set a quantitative limit on measurable recombination frequencies

As the physical distance increases

Horsetail is an example of alloploidy

Asexual but successfully propagates from rhizomes

Telomere

At ends, prevent translocations and are necessary for maintenance of chromosome length

Dominant pattern of inheritance: affected individual will have

At least one affected parent. Does not skip generations

General steps of a viral reproductive cycle

Attachment, entry, integration, synthesis, viral assemble, release

The segment of trp operon immediately downstream from the operator site plays a critical role in

Attenuation

Inheritance patterns of sex linked genes are different than

Autosomal genes

Particulate theory of inheritance

A theory proposed by Mendel. it states that traits are inherited as discrete units that remain unchanged as they are passed from parent to offspring

A karyotype can be used to detect

Abnormal chromosome number or structure, but not small changes of a few to a few thousand nucleotides

Abberant recombination

Abnormal crossing over may cause deletions, duplications, translocations, and inversions

Chromosome duplication is usually caused by

Abnormal events during recombination. Called non allelic homologous recombination. Repetitive sequences can cause this

Duplication-portion of chromosome is repeated. Usually caused by

Abnormal events during recombination. Misaligned during crossing over resulting in a chromosome with a duplicated region and a chromosome with a deletion. Called non allelic homologous recombination. Repetitive sequences can cause this

Spontaneous cause of mutation

Abnormalities in cellular or biological processes. Chemical changes, oxidative stress, trinucleotide repeat expansion

Polyploidy is more common in plants

About 47-70% of plants are polyploidy. They are important in agriculture because it grows a larger and more robust plant

Number of loops in compacted chromosomal DNA varies

According to chromosome size and species

Termination in eukaryotes

According to the allosteric or torpedo model

Maternal effect is a phenomenon due to

Accumulation of gene products that the mother provides to her developing eggs

Genome size variation is not because of extra genes, it's due to

Accumulation of repetitive DNA sequences

Histones can be modified multiple ways

Acetylation, methylatin, phosphorylation

Horizontal gene transfer has dramatically contributed to the phenomenon of

Acquired antibiotic resistance

Three stages of CRISPR-Cas system

Acquisition, expression, interference

Examples of intercalating agents

Acridine dyes and proflavin

Insulator sequences that bind proteins which

Act as a barrier to chromatin or histone remodeling. Block effects of enhancers by formation of loops

Inhibitors bind to

Activators and prevent them from binding to DNA

Regulatory proteins that increase the rate of transcription are termed

Activators and the sequences they bind to are enhancer elements

Regulatory transcription factors

Activators or repressors. Serve to regulate the rate of transcription and influence the ability of RNA pol to begin transcription of a particular gene

Segment polarity genes become

Active in a band of cells that extends around the embryo's circumference to divide it

TFIIH

Acts as a helicase to form an open complex. Phosphorylates the CTD of RNA polymerase II

DNA supercoiling

Acts to further compact the chromosome using twisting forces. The loops are twisted even more

Defense mechanism of CRISPR-cas occurs in three phases

Adaptation, expression, and interference

Ion torrent/proton

Add each base one at a time and monitor release of protons. Cross between a PCR machine and a micro-pH meter. Cheap and no need to separate reaction products

Tailing in bacteria

Added to the 3' end; promotes degradation

Tailing in eukaryotes

Added to the 3' end; promotes stability

Genomic imprinting is indicated by

Addition of methyl bases

The symmetry break that occurs is due to localization of

CTCFs to one X chromosome

Mediator appears to regulate the ability of TFIIH to phosphorylate

CTD and phosphorylate the CTD itself. Plays a pivotal role in the switch between transcriptional initiation and elongation

Inheritance patters of X linked genes differ from autosomal genes

Called X linked inheritance

The mutation rate for a given gene is not constant

Can be increased by the presence of mutagens

DNA that is made from RNA is called complementary DNA (cDNA)

Can be single or double stranded

lac repressor must bind to two of the three operators to cause repression

Can bind to O1 and O2, or O1 and O3, but not O2 and O3

Southern blotting has several uses

Can determine copy number of a gene in a genome, can detect small gene deletions, can identify gene families, can identify homologous genes among different species, segregation analysis

Chain elongation occurs in the 5' to 3' direction by

Addition of one nucleotide at a time to the 3' end (-OH group). As the nucleotide is added, the 2 terminal phosphates are cleaved off

Regulatory elements/operator sites

Affects gene regulation

Example of human mitochondrial disease: LHON

Affects the optic nerve. May lead to progressive loss of vision in one or both eyes. Caused by mutations in several different mitochondrial genes

A typical PCR involves 20-35 cycles of replication

After 20 cycles, a DNA sample will increase 1 million fold, after 30 cycles, a DNA sample will increase 1 billion fold

Expression phase of crispr defense

After adaptation, exposure results in expression of crisp, tracr, and cas9 genes are transcribed and form two non coding RNAs: pre-crRNA and tracrRNA

Maternal effect gene products placed in the eff during oogensis are activated

After fertilization

Duplicated genes accumulate mutations that alter their function

After many generations, they have similar but distinct functions. They are now members of a gene family

Deamination of 5-methyl cytosine poses a problem for repair enzymes

Cannot determine which of the bases on the two DNA strands is incorrect. For this reason, methylated cytosine bases tend to create hotspots for mutation

DNA and RNA can be transferred from gels to membrane either by

Capillary transfer or electrophoresis

Cri-du-chat syndrome

Caused by a deletion in the short arm of chromosome 5

Induced cause of mutations

Caused by environmental agents (mutagens) that may be chemical or physical

Induced mutations

Caused by environmental agents. Agents known to alter DNA are called mutagens

Non coding RNAs in human disease can cause cartilage hair hypoplasia

Caused by mutation in a ncRNA which functions as a ribozyme in the RNaseMRP complex

Malaria

Caused by plasmodium, a protozoan parasite with two main parts to its life cycle: one in a mosquito and one inside red blood cells

Igf-2- is a mutant allele that makes a defective protein

Causes a mouse to be dwarf, but only if inherited from the father

siRNA can inhibit transcription by

Causing chromatin modifications

Nucleosomes are formed from the association of

Chromosomal DNA and the histone proteins

Monosomy

Chromosomal abnormality consisting of the absence of one chromosome from the normal diploid number

Monosomy

Chromosomal abnormality consisting of the absence of one chromosome from the normal diploid number (2n-1)

Reciprocal translocations arise by two different mechanisms

Chromosomal breakage and DNA repair, and non homologous crossovers

Inheritance patterns that deviate from Mendels law are seen when the genes are on the same

Chromosome

Non histone proteins bind to the linker region and aid in

Chromosome compaction and affect gene expression

Staining reveals banding patterns from

Chromosomes

Chromosome theory of inheritance

Chromosomes contain the genetic material. They're replicated and passed from parent to offspring. Nuclei of most eukaryotic cells contain chromosomes in homologous pairs. In the formation of haploid cells, chromosomes segregate independently. Each parent contributes one set of chromosomes

Inheritance patterns that deviate from Mendels law are seen when there are more than two alleles for a gene that

Controls a trait

Mediator acts to mediate the interactions between RNA pol II and regulatory transcription factors

Controls whether RNA pol II can progress to the elongation stage

Operon allows a bacterium to

Coordinately regulate a group of genes encoding proteins that are involved in a common process

DNA replication requires

Coordination with cell division, a origin of replication, DNA polymerases, accessory enzymes

Retroviruses

Copies made from provirus

Unlike chromosomes, chloroplasts are randomly distributed to

Daughter cells

DNA polymerase III synthesizes a

Daughter strand of DNA

Newly made DNA strands are

Daughter strands

Base analogs become incorporated into

Daughter strands during DNA replication. For example, a thymine analogue can be incorporated into DNA instead of thymine

Down promoter mutations

Decrease transcription. Increasing of binding of a silencing element to a negatively regulating transcription factor or removing binding site of something that will promote transcription

DNA methylation is associated with

Decreased gene expression

The binding of a transcription factor to a silencer

Decreases the rate of transcription. Down regulation

Segment polarity mutations

Defects in one side of each segment

Control of gene expression is used in multicellular organisms to

Define tissues and cells with specific functions within the organism

Expressivity

Degree at which a trait is expressed (variable). Environment may influence level of expression or modifier genes may influence phenotype

Gap gene mutations

Delete gaps in the segmentation pattern

Primary ways chromosome structure can be altered

Deletion, duplication, inversion, translocation

Duplications tend to have less harmful effects than

Deletions of comparable size

Variation in chromosome structure

Deletions/duplication, translocations (simple and recirprocal), inversions

PCR

Denaturation of the two strand of DNA, the primers hybridize and allow complementary strands to be synthesized, then elongated and repeated

Three steps of PCR

Denaturation, annealing, extension (synthesis)

Most common chemical change

Depurination

Spontaneous mutations can arise by three types of chemical changes

Depurination, deamination, and tautomeric shifts

Spontaneous chemical changes

Depurination, deamination, tautomeric shift

Norm of reaction

Describes the range of phenotypes seen across different environmental effects (for a given genotype)

Pedigree analysis is commonly used to

Determine the inheritance pattern of human genetic diseases

When deletions have a phenotypic effect they are usually

Detrimental

Many epigenetic modifications are normal parts of

Development

Transcriptional networks regulate

Development by generating patterns of gene expression. Work in cascades

Dd snail mothers produce

Dextral offspring even if the offspring are dd

Empirical approach

Didn't start with a hypothesis to explain the formation of hybrids. Believed that a quantitative analysis of crosses might reveal a mathematical relationship

Cells that do not have a vector will

Die in the presence of the antibiotic

Genetic variation

Difference in alleles and chromosomes. Can be between same or different species

Genetic variation

Differences in alleles and chromosomes, either between members of the same species or between different species

SMART sequencing

Different fluorochromes onto each base. Attached to a phosphate that is cleaved off the dNTPs and ends up in the pyrophosphate product rather than the DNA strand. Flash of light of a wavelenth specific to each fluorochrome is emitted as each base is added

Stable integration of DNA into a vector requires two steps

Digestion of vector and chromosomal DNA to create compatible DNA ends. Covalent joining or ligation of the molecules together (uses the DNA ligase used in replication)

Common types of DNA repair

Direct repair, base excision nucleotide excision repair, mismatch repair, homologous recombination repair, non homologous end joining

3 explanations for over dominance at the molecular/cellular level

Disease resistance, homodimer formation, variation in functional activity

Three explanations for overdominance at the molecular/cellular level

Disease resistance, homodimer formation, variation in functional activity

Intercalating agents

Distort helical structure causing single nucleotide additions and or deletions=frameshift

Intercalating agents

Distort the helical structure. When DNA containing these mutagens is replicated,the daughter strand may contain single nucleotide additions and/or deletions resulting in frameshifts

mRNA or protein products are placed in the developing egg/zygote by mother.

Distributed in a gradient or concentrated in specific regions. Encode proteins that regulate gene expression (transcription factors, receptors)

Maternal effect genes: mRNA or protein that moves into the developing zygote

Distributed in a gradient, encode proteins that regulate gene expression, basic positional information, trans acting

Zygotic genes: segmentation genes

Divide embryo into a series of segments (define number, size, polarity). 3 classes

Pair rule genes

Divide embryo into units of two segments each. Expressed in a series of 7 narrow bands or stripes extending around the circumference of the embryo. Activate segment polarity genes

Segment polarity genes

Divide segments into anterior and posterior regions. Control cellular identity

Initiation of replication in bacteria DNA helicase

DnaB protein and DnaC unwide DNA, separating the strands in both direction beyond the origin

Bacteria genomes have evolved so that their own DNA is modified such that the restriction enzymes that they make

Do no digest it

Nonsense codons

Do not specify an amino acud by signal stop

The trait this is exhibited in the F1 is

Dominant

A lethal allele may produce ratios that seemingly deviate from mendelian ratios. Ex: manx cats

Dominant mutation that affects the spine, mutation shortens the tail in heterozygotes, but is lethal as a homozygote

Z DNA

Double helix structure. Possible biological role in transcription and possible role in chromosome compaction

Semiconservative DNA replication

Double stranded DNA contains one parental and one daughter strand following replication

A nucleosome is composed of

Double stranded DNA wrapped around an octamer of histone proteins

An antisense RNA strand will slightly reduce mRNA but

Double stranded RNA is much better at silencing mRNA

O2 operon operator site for lac repressor

Downstream in the lacZ coding region

Allele E1 encodes an enzyme that functions better a low temps and E2 at higher temps

E1E2 heterozygotes produce both enzymes and therefore have an advantage under a wider temperature range than either E1E1 or E2E2 homozygotes

Targeting polypeptides to the ER membrane by SRP

ER signal sequence. SRP binds to signal sequence, pauses translation, binds to receptor in the ER membrane, GTP hydrolysis causes protein to pass through pore into ER and translation continues

Illumina sequencing

Each base is fluorescently labeled, all have proprietary removable terminators. One base added at a time, imaged to see which base is added, terminator is removed

There are 20 amino acids that may be found in polypeptides

Each containes a different side chain or R group

Diploid organisms have two copies of

Each gene

Dioecious plants

Each individual plant is either male or female

Complementation

Each recessive allele is complemented by a wild type allele. This indicates that the recessive alleles are in different genes

Eukaryotic species contain one or more sets of chromosomes

Each set is composed of several different linear chromosomes

Interference phase of crispr defense

Each spacer in a crRNA is complementary to one strand of the bacteriophage DNA. crRNA acts as a guide that causes the tracrRNA-crRNA-cas9 complex to bind to the strand

Expression vectors often include a leader peptide to facilitate

Easy purification of expressed proteins

Protospacer adjacent motif (PAM)

Effector complex binding site

Interference in CRISPR-Cas

Effector complex binds homologous foreing. DNA base pairing

Termination in bacter

Either rho dependent or independetn

Genomic imprinting occurs during

Gamete formation

Double recombinant

Gametes & offspring resulting from a cross over in both regions of a three point test cross

Zygotic genes

Gap genes, pair rule genes, segment polarity genes, homeotic genes

In metaphase chromosomes, the radial loops are

Highly compacted and stay anchored to a scaffold

Heterochromatin

Highly condensed (non-acetylated). Common around telomeres and centromeres. Tend to have fewer genes and lower recombination frequences

MacroH2A

Histone variant that is found along the inactive X chromosome

Whether or not genes are located on the same chromosome is going to make a difference in terms of

How they assort in meiosis

Both drosophila and arabidopsis have both

Hox and MADS box genes but their functions have diverged over evolution

Homeobox is a DNA binding domain (homeodaomain) that all

Hox genes possess

HOTAIR gene is located on

Human chromosome 12 within a cluster of HoxC genes and is a long ncRNA

Human environmental condition affecting phenotype

Humans with phenylketonuria (PKU) are unable to metabolize phenylalanine. Symptoms include mental retardation. When detected early, individuals can be fed a phenylalanine-free diet and stay healthy

Mendel mated true breeding plants with one trait to plants with a different trait to create

Hybrids

Two polynucleotide strands are held together with

Hydrogen bonding vetween the nucleotide bases

SRP RNA stimulates proteins within both SRP and the SRP receptor to

Hydrolyze GTP. SRP RNA alters the structures of these proteins

Tertiary structure of a ptoetin is determined by

Hydrophoibic and ionic interactions as well as hydrogen bonds and Van der Waals interactions

The color of bacterial colonies will depend on whether or not the B-galactosidase is function

If it is, the colonies will be blue-no insert. If not, the colonies will be white-insert present

Genomic imprinting expression depends on

If its origin is maternal or paternal. Express only the maternal or paternal allele - monoallelic expression

Wobble rule

In codon-anticodon recognition, the first two positions pair strictyl accoring to the AU/GC rule but the third position can tolerate certain mismatches

Natural transformation

In transformation. Occurs in a wide variety of bacteria. DNA uptake occurs without outside help

If a transposable element is inserted into a gene, this will likely

Inactivate the gene

Although the Tsix transcript is initially produced by both X chromosomes the Xist transcript is only produced from the

Inactive chromosome

Latency

Inactive stage of a virus integrated into the host cell genome. Called a prophage or provirus

Nonionizing radiation

Includes UV light and has less energy. Cannot penetrate deeply into biological molecules

Ionizing radiation

Includes X rays and gamma rays. Short wavelength and high energy. Penetrate deeply into biological materials and creates chemically reactive molecules termed free radicals

A heterozygote has a phenotype that is intermediate between either corresponding homozygote

Incomplete dominance

Dominant phenotype is not expressed even though an individual carries a dominant allele

Incomplete penetrance

Repeats (trinucleotide)

Increase in the number of repeats=trinucleotide repeat expansion (TNRE)

Promoters

Increase or decrease transcription

Up promoter mutations

Increase transcription. Increase binding to positively regulating transcription factors

As genes get farther apart the chance of getting two (or more) crossover events between the genes

Increases

Binding of a transcription factor to an enhancer

Increases the rate of transcription. Up regulation

During extension of PCR, the quencher is cleaved off

Increasing fluorescence

When genes are physically associated they do not

Independently assort and will not necessarily follow Mendel's law of independent assortment

Non parentals are predicted only if the genes segregate

Independently of each other

Cystic fibrosis

Individual cannot transport chloride effectively resulting in multiple phenotypes

Combination of maternal effect and gap proteins control

Individual pair rule stripe formation

Inversion heterozygotes

Individuals with one copy of a normal chromosome and one copy of an inverted chromosome

Genes that are regulated by inducers are termed

Inducible

Some viruses have specialized proteins to help

Infection. Spikes and knobs

Opportunistic infections

Infections seen in patients with compromised immune systems

Glucocorticoids

Influence metabolism in most cells

The net effect of a transcription factor is to

Influence the function of RNA polymerase

Inheritance patterns that deviate from Mendels law are seen when the trait is sex

Influenced or limited

An advantage of negative supercoiling in bacteria is that

It promotes strand separation in small regions enhancing DNA replication and transcription

DNA polymerase is processive

It stays clamped onto the DNA template strand and keeps going

A ribosome is composed of

Large and small subunits. Each is formed in the nucleolus from proteins and rRNAs

Random sampling error

Large for small samples and small for large samples

Steps of transformation

Large fragment of DNA binds to surface of cell. Endonuclease enzyme outside the cell cuts up the DNA. One strand of the DNA is degraded, and the other enters the cell. DNA must be incorporated into the chromosome to be stably inherited, results in heteroduplex DNA. Then repaired by DNA repair enzymes. Sometimes transforming recipient to the new genotype

DNA replication is more complicated in eukaryotes because

Large linear chromosomes, tight packaging within nucleosomes, more complicated cell cycle regulation

Lysogeny

Latency in bacteriophage

DNA polymerase III synthesizes the DNA using the RNA primers on both

Leading and lagging strands

Aneurploidy commonly causes an abnormal phenotype

Leads to imbalance in the amount of gene products. 3 copies can lead to 150% production of the hundreds or even thousands of gene products from a particular chromosome

Gene regulation is important for cellular processes such as

Metabolism, response to environmental stress, cell division

Splice junctions in eukaryotes have 2 bases in mRNA that's left behind and 2 bases out

Mutation in intron stops RNA being sliced properly and they get into cytoplasm and creates different protein

lacI-

Mutation in lacI gene. Resulted in the constitutive expression of the lac operon even in the ebsence of lactose

Trinucleotide repeat expansion

Mutation that results in expansion of the number of trinucleotide repeats

Transcriptional repressors inhibit mediator

Prevent switch to elongation stage, preventing transcription

Methylation can repress transcription by

Preventing transcription factors from binding to the DNA

An advantage of CRISPR-Cas is targeting genetic changes

Previous methods usually involve random changes and lots of screening, insertion of new genes in random places

Four levels of structue in proteins

Primary, secondary, tertiary, quaternary

What is needed to make new strands of DNA at the replication fork

Primase, DNA polymerase, and DNA ligase

Annealing in PCR

Primers bind to DNA

MutH can distinguish between the parental strand and the daughter strand

Prior to replication, both strands are methylated. Immediately after replication, the parental strand is methylated but the daughter strand is not

Probe in western blot

Probe is a primary and secondary antibody. Probe is specific to a fragment on the membrane, then protein with the same sequence is there

Lethal allele

One with the potential to cause death. Typically the result of mutations in essential genes and are usually inherited in a recessive manner

A testcross is expected to yield a max of

Only 50% recombinant offsping. Same as if genes were on different chromosomes

Conditional lethal alleles

Only lethal under certain environments

High stringency

Only nearly identical sequences hybridize

Gene redundancy

Only one gene is required for normal phenotype, but multiple versions present

Negative supercoiling

Opposite direction to the spiral of the helix

Eukaryotes also posses

Organelle genomes

Chloroplasts have maternal inheritance

Organelles are inherited only through the egg cytoplasm. Sperm cells do not transmit chloroplasts

Observations that support the endosymbiosis theory

Organelles have circular chromosome (like bacteria). Organelle genes are more similar to bacterial genes than to those found within the nucleus

Inversion heterozygotes

Organisms with one inverted chromosome and one noninverted homolog

Plasmids and viruses used as vectors contain

Origin of replication, a selectable marker, restriction site(s), gene that functions as a visual marker

Small interfering RNAs (siRNAs)

Originate from exogenous sources (not normally made by cells)

Three types of DNA sequences are required for chromosomal replication and segregation

Origins of replication, centromeres, telomeres

Some viruses have a broad host range

Others can infect only a single species or a single cell type

In the F2, the dominant trait plants

Outnumbered recessive trait plants with a 3:1 ratio

Example of sex limited traits: human sexual dimorphism

Ovaries in females, testes in males

Reverse transcriptase PCR (RT-PCR)

PCR can be used to amplify cDNA and potentially quantify RNA transcripts in living cells

In situ hybridization

Probe tissues with labeled DNA to visualize gene expression. 7 developmental genes visualized by in situ hybridization

Transformation

Process by which a bacterium will take up extracellular DNA released by dead bacteria. Uptake of DNA from the environment

Differentiation

Process by which a cell achieves final form and function

Differentiation in development

Process by which a cell becomes a very specialized and committed type

Crossing over

Process in which homologous chromosomes exchange portions of their chromatids during meiosis

X chromosome inactivation

Process that occurs in female mammals in which one of the X chromosomes is randomly turned off in each cell. Which X is chosen at random in different cells early in development

Polyploid plants having an odd number of chromosome sets are usually sterile

Produce highly aneuploid gametes

Cyclic AMP

Produced from ATP by the enzyme adenylyl cyclase. Binds an activator protein known as the catabolite activator protein

Individuals carrying balanced translocations have a greater risk of

Producing gametes with unbalanced combinations of chromosomes. Depends on the segregation pattern during meiosis I

RNA polymerase has many components, nut the sigma factor is what recognizes

Promoter regions in bacteria

The lac operon regions

Promoter, CAP site, operator, protein coding genes, terminator

Mutations in noncoding sequences

Promoters, splice junctions, 5' 3' UTR

Telomerase contains

Protein and RNA. The RNA is complementary to the DNA sequence of the telomeric repeat, allowing telomerase to bind to the 3' overhang

Virus assembly in viral reproduction

Protein and nucleic acid subunits come together to make infectious particles. Some viruses self assemble, some use proteins to help assembly

Genes that encode polypeptides are

Protein coding genes or structural genes. They are transcribed into messenger RNA

A typical bacterial chromosome contains a few thousand genes

Protein encoding genes, intergenic regions

All viruses have a caspid composed of

Protein subunits called capsomers (can be helical or polyhedral). Some have a viral envelope

RNA has been historically studied for its role in making

Proteins

Torpedo model for eukaryotic termination

RNA cute near polyA signal sequence, exonuclease causes complex disassociation

MicroRNAs (miRNAs)

RNAs that are transcribed from genes and from a hairpin structure

Transcription termination

RNA polymerase stops synthesizing RNA. A terminator is reached that causes RNA polymerase and the RNA transcript to dissociate from the DNA

Histones are needed for the compaction of

Radial loops

Transcription elongation

RNA polymerase synthesizes RNA. RNA polymerasae slides along the DNA in an open complex to synthesize RNA

Mutant allele is due to

Random mutations that occur in DNA or induced by scientists

The selection of which chromosome is inactivated is a

Random process

The larger the sample size, the more closely observed results will match expected outcomes. This is due to

Random sampling error

Cycle threshold Ct

Reached when the accumulation of fluorescence is higher than background

Modern Sanger DNA sequencing

Reactions occur in a single tube with each of the 4 ddNTPs labeled with different fluorescent dye

Oxidative stress

Reactive oxygen species can cause damage to DNA

Inborn error of metabolism

Realtionship between inheritance of the trait and the inheritance of a defective enzyme

Hox transcript antisense intergenic RNA (HOTAIR)

Recently discovered ncRNA that alters chromatin structure

Most random mutations produce

Recessive alleles

Target site primed reverse transcription

Retrotransposon transcribed into RNA with a poly A tail, and target DNA is nicked. RNA binds to the nicked site by AT base pairing. Reverse transcriptase makes a DNA copy of the RNA, Endonuclease makes a second cute nearby. Retrotransposon DNA is ligated into the target site

DNA demethylating agents and histone deacetylase inhibitors

Reverse epigenetic silencing of miRNAs that behave as tumor suppressors

Copying RNA into DNA uses

Reverse transcriptase

Retroelements transpose via an RNA intermediate and movement requires two enzymes

Reverse transcriptase and integrase

3 major epigenetic mechanisms

Reversible modification of DNA by addition/removal of methyl groups. Alteration of chromatin by addition/removal of chemical groups to histone proteins. Regulation of gene expression by small, noncoding RNA molecules

The RNA produced has sequences that regulate its function

Ribosomal binding site and start and stop codons

rRNA involved in protein synthesis

Ribosome components (80% of total cellular RNA)

Translation occurs on the surface of large macromolecular complexes

Ribosomes

Eukaryotic ribosome

Ribosomes in the cytosol

Untranslated RNAs that become part of protein RNA complexes

Ribosomes, signal recognition particles, spliceosomes, RNase P, telomerase

Trans acting factors

Regulatory proteins that bind to cis acting elements. They are located elsewhere in the DNA, often a different chromosomes.

Small effector molecules may modulate

Regulatory transcription factor activity

Nucleosome arrangements around promoters are affected by

Regulatory transcription factors and nucleosome/histone modifications

Receptors for steroid hormones are

Regulatory transcription factors inside cells. Hormone binds to its receptor and complex then acts as a transcription factor

LTR retrotransposons

Related to retrovirus. Move around genomes, but cannot produce viral particles. Contain long termina repeats at both ends. Encode reverse transcriptase and integrase

In lower eukaryotes, genes are

Relatively small and contain primariy sequencing encoding polypeptides. Very few introns

DNA topoisomerase I

Relaxes negative supercoils, breaks one strand and rotates the DNA

Stop codons aren't recognized by tRNAs but by proteins called

Release factors

Depurination

Removal of a purine (G or A). Covalent bond between deoxyribose and a purine base is unstable. Undergoes a reaction with water that releases the base from the sugar

Two different directions a shell and internal organs can twist

Right handed (dextral) more common. Left handed (sinistral)

Small nuclear RNA functional role

RNA processing

Allosteric model for eukaryotic termination

RNA synthesis stops near polyA signal sequence due to transcriptional complex disassociating

Allosteric model

RNA synthesis stops near polyA signal sequence. Proteins lost from transcriptional complex causing it to disassociate

Deamination

Removal of an amino group from the cytosine base turning a C into a U and pairing up with A instead of G. DNA repair enzymes can recognize uracil as an inappropriate base in DNA and remove it

Depurination

Removal of purine resulting in apurinic site. Easily fixed but can be replicated. Most common chemical change

DNA polymerase can not

Remove RNA primer from Okazaki fragments. DNA polymerase I removes the primers and fills in gaps

Photolyase

Repair thymine dimers-splits dimer and resorts DNA

Recombination repair

Repairing double stranded breaks of entire chromosomes

Alkyltransferase in direct repair

Repairs alkylated bases. Transfers methyl or ethyl group from base to a cysteine side chain within the alkyltransferase protein. Permanently inactivates akyltransferase

Alkyltransferase

Repairs alylated bases-transfers methyl/ethyl group from C to self

Large genomes contain a huge number of

Repeat sequences. About 50% repetitive DNA in the human genome

Polytene chromosomes undergo

Repeated rounds of replication without cell division. The doubling produces a bundle of chromosomes that lie together in a parallel fashion

Several human genetic diseases are caused by trinucleotide repeat expansion (TNRE)

Repeats increase from one generation to the next. Include spinal and bulbar muscular atrophy, Huntington, fragile X

Most of the variations in genomes between organisms is due to differences in

Repetitive DNA

ATP dependent chromatin modification is a protein complex that uses ATP to

Reposition nucleosomes, remove nucleosomes, change nucleosome composition

Cap binding proteins

Required for the proper exit of most mRNAs from the nucleus. Recognized by initiation factors that are needed during the early stage of translation. Important in the efficient splicing of introns particularly the intron closest to the 5' end

RNA primers

Required to prime (start) the process of replication

Gene regulation in eukaryotes enables them to

Respond to changing environmental conditions and express sub sets of genes needed at particular times in life and cell cycles

Why we need to regulate gene expression

Response to the environment, metabolism, cell division

Enzymes used to cut DNA are known as

Restriction endonucleases or restriction enzymes

Enzymes used to study DNA

Restriction enzymes, DNA polymerases, DNA ligases

Spontaneous mutations

Result from abnormalities in cellular/biological processes. Ex: errors in DNA replication

Unlike nuclear genes, organellular genes are not inherited from both parents

Results in non mendelian results from reciprocal crosses

Complete nondisjunction

Results in one diploid cell and one without chromosomes. The chromosome-less cell is nonviable

lacI- mutation either

Results in synthesis of an internal activator or eliminates the function of the lac repressor that can diffuse throughout the cell

Disease resistance

Slightly reduced protein function, but altered protein prevents infection (i.e. sickle cell)

O3 operon operator sire for lac repressor

Slightly upstream from the promoter

Flap endonuclease removes

Small RNA flaps generated by DNA polymerase delta

Inducers

Small effector molecule that in some cases may increase transcription

Activator and repressor proteins can be bound and affected by

Small effector molecules

Each snRNP contains

Small nuclear RNA and a set of proteins

snRNA

Small nuclear RNA involved in mRNA processing

snoRNA

Small nucleolar RNA processing of rRNA

Transposition involves integration of

Small segments of DNA into chromosomes. Can occur at many different locations within the genome

Red blood cells of heterozygotes tend to rupture when infected by plasmodium, preventing propagation of the malaria parasite and providing resistance

So HbA HbS individuals are better that HbS HbS and HbA HbA

As soon as an mRNA strand is long enough, a ribosome will attach to its 5' end

So translation begins before transcription ends

SDS page

Sodium dodecyl sulphate polyacrylamide gel electrophoresis. Denatures proteins and coats them with vely charged SDS. Separate based on size alone

Human mitochondrial diseases can arise from mutations that occur in

Somatic cells during aging. Mitochondria are especially susceptible to DNA damage from free radicals

Translesion DNA polymerases

Specialized DNA polymerase that is able to replicate DNA through distorted structures and bulky lesions that halt other DNA polymerases; often makes more errors during DNA synthesis than other DNA polymerases

Mutation rates vary substantially between

Species and even within different strain of the same species

Population level

Species traits are selected based on survival and reproduction

Genome size vary greatly between

Species. Variation doesn't necessarily relate to complexity

The trans acting factors (MADS-Box transcription factors) bind to

Specific cis elements activating and repressing 100s of different genes which in turn leads to the development of the different floral organs

De novo methylation

Specific genes are methylated in gametes from mother or father. The methylation of DNA that was previously unmethylated

Alternative splicing is not random

Specific pattern of splicing is regulated in a given cell

Imprinting involves methylation of

Specific regions of DNA

At the cellular level development has three main events

Specification, determination, differentiation

Start codon in mRNA

Specifies the first amino acid in a polypeptide sequence

To get the chi square

Take the observed minus expected squared over expected then add all those up for each

Self fertilization of autopolyploidy will result in

Tetraploid (4n) offspring

Two common protein complexes that communicate the effects of regulatory transcription factors are

TfIID and mediator

CRISPR has a guide RNA

That allows the Cas9 to cut where the guide RNA has laid it out. Making it very precise

HOTAIR acts as a scaffold

That guides two histone modifying complexes to their target genes for scilencing

Positive regulation: has an activator bound to the activator binding site

That leads to transcription

Osmoregulation

The ability to control the amount of water inside the cell

The progression from the primary to the 3D structure is dictated by

The amino acid sequence withing the polypeptide

Base modifiers cause modified bases to not pair with

The appropriate nucleotides in the daughter strand during DNA replication

Breakpoint

The are of break, and if a gene is within it, then expression is affected (position effect)

For some bacterial genes, the translation of mRNA us regulated by

The binding of proteins

Steroid hormones are secreted into

The bloodstream

Pair rule genes establish

The boundaries of segments, then program the developmental fate of the cells within each segment by controlling expression of segment polarity genes

70% of all miRNAs are expressed in

The brain and many are specific to neurons

A chromosomal rearrangement may affect a gene because

The breakpoint occured within a gene

In detailed genetic maps, the locations of genes are mapped relative to

The centromere

Binding of sigma factor of the holoenzyme to the promoter forms

The closed complex

The anticodon is antiparallel to

The codon

What governs the overall supercoiling of bacterial DNA?

The competing action of the enzymes DNA gyrase and DNA topoisomerase I

DNA replication relies on

The complementarity of DNA strands. The AT/GC rule

Transposase

The enzyme that catalyzes the removal of a transposable element and its reinsertion at another location

Relaxase

The enzyme used to nick the F plasmid, guiding one strand to a DNA pump

Aminoacyl-tRNA synthetases

The enzymes that attach amino acids to tTRNAs. 20 types for each amino acid

Cap binding proteins play roles in

The export of some RNAs to the cytoplasm, early stages of translation, splicing of introns

Termination in translation

The final stage occurs when a stop codon is reached in the mRNA

Intergenic suppressor may be a second protein that takes on the role of

The first

Specification

The first cues confer spatially distinct identity

Nonionzing radiation causes

The formation of cross linked thymine dimers which may cause mutations when that DNA strand is replicated

Attenuation inhibits

The further production of tryptophan

With an even number of crossover events the DNA between the genes is exchanged but

The genes remain on the same chromosome. These are not counted as recombinations because they look like the parents even though crossing over occurred

Genes that control development in drosxophilia act in a temporarily and partially ordered cascade starting with

The genes that establish the anterior-posterior axis of the embryp

Transcription

The genetic information in DNA is copied into a nucleotide sequence of RNA

The maternal effect refers to the fact that the phenotype of the offspring is dependent on

The genotype of the mother

In an inversion, the amount of genetic information stays the same. Hence,

The great majority of inversions have no phenotypic consequences

By combining many different cis regulatory elements to control each gene

The huge array of expression patterns needed to generate complex multi cellular organisms can be achieved

DNA helicase breaks

The hydrogen bonds between the DNA strands

Two regions near the Igf2 gene where DNA methylation occurs

The imprinting control region and the differentially methylated region

Extranuclear inheritance

The inheritance of genetic material that is not found within the nucleus (generally inherited from the mother). Mitochondria and chloroplasts

Initiating translation in bacteria

The initiator tRNA recognizes the start codon in mRNA.

A third level of compaction after nucleosomes and fiber involves

The interaction between the fibers and the nuclear matrix

Mediator proteins mediates

The interactions between transcription factors and RNA polymerase

Nucleotide bases (ATCG) are in

The interior. The bases are stacked

A mutation in a trans acting factor is complemented by

The introduction of a second gene with normal function

Group I and II differ in the way that

The intron is removed and the exons reconnected

Repressor from the F factor can diffuse and turn off

The lac operon on the bacterial chromosome

C-value paradox

The lack of correlation between genome size and organism complexity

In each cycle of elongation a peptide if formed between

The last amino acid in the chain and the amino acid being added

Simple mendellian inheritance describes inheritance patterns that obey

The law of segregation and the law of independent assortment

Origin of transfer

The location on an F factor or within the chromosome of an Hfr strain that is the initiation site for the transfer of DNA from one bacterium to another during conjugation

Example of haplodiploid in honey bees

The male is produced from unfertilized eggs that are haploid (one set of 16 chromosomes) and the females grow from fertilized eggs that are diploid (two chromosome sets, 32 total). So only the female arises through sexual reproduction

Genomic imprintin

The maternal Igf2 ellel is silences but the paternal allele is active

Sex determination

The mechanism by which an individual develops into a female or a male

Dosage compensation

The mechanism that keeps levels of expression of X chromosome genes i n balance with those of autosomal genes for both sexes

When miR-200 is expressed at normal levels

The miRNAs inhibit EMT (E-cadherin remains high) so tumors can't metastasis as easily

In linked, the parental phenotypes are observed more than expected in the F2 and

The mixed phenotype is observed less than expected

When a bacteriophage infects a cell it can cause the host DNA to become frangmented

The pieces of the host chromosome can get packaged with the bacteriophage protein

Chromatin remodeling complexes lead to changes in

The position and composition of nucleosomes

Germ cells form at

The posterior pole of the embryo and nuclei in other regions form somatic cells

Capping occurs as

The pre mRNA is being synthesized by RNA pol II. Usually when transcripts is only 20 to 25 bases long

Secondary structure of a protein

The primary structure of a protein folds to form regular, repeating shapes known as secondary structures

DNA helicase and primase are physically boudn to each other to from a complex called

The primosome. Leads to the way at the replication fork

Product rule

The probability that two or more independent events will occur is equal to the product of their respective probabilities

The non mendelian inheritance pattern of maternal effect genes can be explained by

The process of oogenesis

Some transcriptional activators recruit chromatin remodeling enzymes and histone modifying enzymes to

The promoter

Recessive mutant alleles typically produce less functional protein because

The protein is defective or they produce lower levels of the functional protein

Mendels law of independent assortment can be explained by

The random alignment of homologous chromosomes during meiosis

With X-0 sex determination even with XY male, what determines the sex?

The ratio of X chromosomes to autosomes

Since a cell may have different types of mitochondria, whether the cell is affected depends on

The ratio of mutant to normal mitochondria

Frameshift mutations shift

The reading frame to a different sequence downstream from the mutation (and very often terminates early)

Initiation of replication in bacteria other proteins cause

The region to bedn around the DnaA proteins and separate the AT-rich region

Breakpoint

The region where two chromosome pieces break and rejoin with other chromosome pieces

Maps created by recombination analysis estimate

The relative distances between linked genes. Based on the number of times that a crossover event occurs between genes. Creates a linkage map

Hydrolysis of GTP is essential for

The release of SRP for translation to resume

In expression, a region of the tracrRNA is complementary to

The repeat sequences of the pre-crRNA so they pair up

Nucleosomes

The repeating structural unit within eukaryotic chromatin. Shortens the DNA 7 fold

The leading strand is made in the same direction as

The replication fork

Human cleidocranial dysplasia (CCD)

The result of a mutation in the human CBFA gene, the homolog of runt. Characterized by numerous skeletal defects, including no collar bones

Testcross

The result of breeding a recessive homozygote with an organism of dominant phenotype but unknown genotype. Heterozygote X and homozygote recessive

Since most mutations are deleterious, DNA repair systems are vital to

The survival of all organisms

Wobble base

The third base that is the degenerate base

The size and location of the mosaic region from mitotic nondisjunction depends on

The timing and location of the original abnormality. Most severe example is when abnormality occurs during the first mitotic division after fertilization

A single type of micro RNA inhibits

The translation of several different mRNAs through partial complementarity. Because the matching with the mRNA only has to be about 80% the same to the miRNA

Conditions that favor formation of the 3-4 stem loop rely on

The translation of the trpL mRNA

Simple transposition

The transposable element is removed from the original site and transferred to a new site by a cut and past mechanisms. These are called transposons

Exon shuffling

The variation in the patterns by which RNA may produce diverse sets of exons from a single gene

Quaternary structue of a proteinn is formed when

The various polypeptides associate together to make a functional protein

The organisms that show the greatest variation in genome sizes are

The vascular plants

Leaf variegation on mirabilis jalapa is a result of

The way chloroplasts segregate during mitosis

Bacterial cells have one type of ribosome in

Their cytoplasm

The sequence of DNA in a gene is not always colinear with

Their functional mRNAs

The closer the genes are to one another, the lower the chance of

Them undergoing crossing over

If region 1 does not bind to region 2

Then region 2 can bind to region 3 and region 4 can not bind to region 3

If region 1 binds to region 2

Then region 3 can bind to region 4

The three genes exist as two alleles each

There are then 2^3=8 possible combinations of offspring

Transduction

Transfer DNA between bacteria cells through viruses

Conjugation

Transfer of DNA from one bacterium to another following direct cell to cell contact. Direct transfer between cells

Horizontal gene transfer

Transfer of genes between organisms. May occur within or between species. Many bacterial genes are derived from horizontal gene transfer

Vertical gene transfer

Transfer of genes from mother to daughter cell or from parents to offspring

RNA binding proteins regulate

Translation

tRNAs carry amino acids at the 3' end for

Translation

In bacteria the shine delgarno sequence facilitates ribosome binding

Translation initiation in bacteria

Antisense and double stranded RNA can inhibit

Translation of mRNA

Regulation of gene expression can be

Translational or post-translational

Special polymerases help with translesion synthesis

Translesion polymerases contain an active site with a loose flexible pocket to accommodate the abnormal DNA structure. They have low fidelity

Theory: inheritance patterns of traits can be explained by

Transmission patterns of chromosomes during meiosis and fertilization

Retrotransposition

Transposable element is transcribed into RNA, then reverse transcriptase makes a second copy in DNA. These are called retrotransposons or retroelements

All animal species have evolved ncRNAs as a defense against

Transposable elements

PIWI interacting RNAs silence

Transposable elements in animals

Nonhomologous recombination

Transposable elements insert into DNA that has no sequence homology with the transposon

Must human transposons appear to be inactive, but it is possible for a mobile element to

Transpose from one chromosome to another in gamete-forming cells of the mother, causing a genetic disease

At the molecular level, overdominance is due to

Two alleles that produce slightly different proteins

An individual with a reciprocal translocation usually produces 4 types of gamete

Two are viable and two are nonviable. This is termed semi-sterility

An octamer is composed of

Two copies each of four different histones

For a given character, a pea plant contains

Two discrete hereditary factors, one from each parent. The two factors may be identical or different

Non homologous end joining

Two ends are simply pieced back together

In receprical translocations

Two non-homologous chromosomes exchange genetic material

Gene interactions occur when

Two or more different genes influence the outcome of a single trait

Gene interactions

Two or more different genes influence the outcome of a trait

Linked or linkage

Two or more genes do not independently assort and tend to be transmitted together

Gene families

Two or more genes that are homologous that were derived from the same ancestral gene

Duplications can provide additional genes, forming gene families

Two or more genes that are similar to each other

Paralog

Two or more homologous genes within a single species

Homodimer formation

Two slightly different proteins may have better functionality when bound

Chromosome structure alteration: reciprocal translocations

Two way transfer. Two nonhomologous chromosomes may exchange bits of chromosome and lead to a new karyotype

The nucleosome free region is flanked by

Two well positioned nucleosomes the -1 and +1 nuclesomes. They mark the transcription start sites

Translocation down syndrome

Type of down syndrome caused by rearranged chromosome material. There are 3 copies of chromosome 21, but one is attached to another chromosome instead of being separate

Riboswitches

Type of regulation found in prokayotes and eukaryotes. RNA can exist in two different confirmations. One is active and one is inactive

Explansion of trinucleotide repeats may be within the coding sequence of the gene

Typically CAG (glutamine). Encoded protein contains long tracks of glutamine which causes the proteins to aggregate and is correlated with disease progression

The genome of bacteria

Typically a single circular chromosome

Variations in chromosome structure and number

Typically affect more than one gene, important in evolution, can cause disease, important for new strains of crops

The primary structure of an RNA strand is much like DNA but

U instead of T, and ribose instead of deoxyribose

Because of there being even numbers of crossover events, observed recombinations tend to

Underestimate the actual measure of map distance

Genetic maps are useful in many ways including

Understanding genome of a species, cloning genes, inferring evolutionary relationships, understanding human disease, agriculture and selective breeding

Three main types of DNA sequences

Unique or non repetitive, moderately repetitive, highly repetitive

After associating with PAM Cas9

Unwinds adjacent DNA allowing sgRNA to pair with the DNA. Once paired Cas9 cuts the DNA

Deamination of 5-methyl cytosine can occur but does not result in

Uracil. It results in thymine

Ligation

Use ligase to "glue" your gene of interest into the vector

Restriction digest

Use restriction enzymes to cut the plasmid at a specific site

Aneuploidy

Variation in the number of particular chromosomes within a set. Regarded as abnormal. Ex: trisomy (2n+1) and monosomy (2n-1)

Aneuploidy

Variation in the number of particular chromosomes. Leads to imbalance in the amount of gene product

Allelic variation

Variations in specific genes

Allelic variations

Variations in specific genes. Typically single or a few nucleotide changes

Trait or variatn

Version of the character such as tall or dwarf

Methylation in many eukaryotic species, but not all

Vertebrates and plants have abundant DNA methylation

If the genes are close together

Very few recombinant offspring

DNA replication must occur

Very quickly, very accurately, at the appropriate time in the cell cycle

Alternate segregation

Viable and balanced. Chromosomes on opposite sides of translocation cross segregate into same cell

Provirus

Viral DNA that inserts into a host genome

Entry in viral reproduction

Viral genome enters the cell. Either viral genome alone or viral genome with associated proteins. Some viral proteins are immediately produced

Sources of siRNA can be

Viruses that infect a cell, or researchers can make them to study gene function experimentally

Bacteriophage

Viruses that specifically attack bacteria. Composed of genetic material surrounded by a protein coat

Retroviruses

Viruses that use reverse transcriptase to copy RNA into DNA for integration into host cell genome (HIV for example)

SDS page vs western blot for seeing proteins

Western is specific for a protein and SDS is the whole length of protein

Host range differences between viruses

What species a virus can infect and the cells that a virus infects are its host cells

Epistasis

When a gene can mask the phenotypic effects of another gene. A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited

Overdominance

When a heterozygote is more vigorous than the two homozygotes (aka heterozygote advantage)

There is not one specific promoter sequence but

There is similarity or consensus sequences

Accumulation before fertilization allows development to proceed very quickly after fertilization

Therefore defective alleles in maternal effect genes tend to have a dramatic effect on the phenotype of the individual

E1E2 heterozygotes prodcue both enzymes

Therefore have an advantage under a wider temperature range than either E1E1 or E2E2 homozygotes

Reverse transcriptase lacks a proofreading function

Therefore mutant strains arise frequently. Difficulty for immune system to fight off. Resistant to antiviral drugs

Machine where PCR is done

Thermocycler

Transposable elements are flanked by direct repeats, also called target site duplications

These direct repeat sequences in the same direction on both sides

Genes may have sequences for many different regulatory transcription factors

These may overlap so that the binding of a sequence by one transcription factor may preclude the binding of others. The result in terms of transcription is dependent on what sites are occupied

Maturing animal oocytes are surrounded by maternal cells that provide them with nutrients

These nurse cells are diploid, whereas the oocyte becomes haploid

As with mitochondria, some chloroplast proteins are encoded by genes in the nucleus

These proteins contain chloroplast targeting signals

The most common way to regulate gene expression in prokaryotes (and eukaryotes) is at the level of

Transcription initiation. The rate of RNA synthesis is increased or decreased

Bacterial translation can begin before

Transcription is completed

Combinatorial control

Transcription is controlled by many factors

Binding of proteins to control or regulatory elements affects

Transcription of as associated gene

Synthesis of viral components in viral reproduction

Transcription of viral genes, translation of viral proteins, synthesis of more copies of viral nucleic acid

Order of microRNA biosynthesis

Transcription produces pri-miRNA, folding of pri-miRNA into loop, processed by drosha and exported from nucleus by exportin 5, pre-miRNA or pre-siRNA digested by dicer, RISC RNA complex binnds to mRNA targets, mRNA shuttled to Pbody or degraded

Gene regulation in eukaryotes can occur at different points in the pathway of gene expression such as

Transcription, rate of translation including microRNA control, protein modification, stability of mRNA and protein

Riboswitches can be a form of control for

Transcription, translation, RNA stability, splicing

Regulatory proteins control

Transcription. Rate of RNA synthesis is changed

Histone acetylation makes genes on nucleosomes available for

Transcription. This is reversible and acetyl groups can be removed changing the chromatin from an open to closed conformation

Cell-cell interactions influence

Transcriptional programs and the developmental fate of cells during embryonic development

Prokaryote gene regulation is mainly done in

Transcritpion

Open conformation of chromatin

chromatin is highly extended and transcription can take place

CRISPR-Cas9 requires 2 RNA molecules

crRNA + tracerRNA. Pair and combine with Cas protein to form an effector complex

In expression, the pre-crRNA is cleaved into many small molecules no called

crRNAs

In bacteria the intitiator tRNA is designated tRNA fmet

It carries a modified methionine, N-formylmethionine

The chi square test does not prove the hypothesis is correct

It evaluates whether or not the data and the hypothesis have a good fit

Plants with alloploidy may be more vigorous because

It has a mixture of traits from two species rather than one

Structure of trp operon is similar to the lac operon

It has a regulatory region, operator, promoter

tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome

Structural genes of trp operon

trpA through E encode enzymes involved in trytophan biosynthesis

The first gene in the trp operon is

trpL

Non coding RNAs affect translation and stability of

mRNA

The initiator tRNA recognizes the start codon in

mRNA

Anticodonn region of tRNAs interacts with

mRNA and must be exposed

piRNA sequences are complementary to

mRNA from a transposable element

Poly A is important for

mRNA stability and translation

Researchers had used antisense RNA to inhibit

mRNA translation. But also found that antisense RNA also inhibited mRNA expression

Initiation stage of translation

mRNA, initiator tRNA and ribosomal subunits associate to form an initiation complex

In most cell types, ncRNAs are more abundant than

mRNAs

The genetic material in mitochondria is referred to as

mtDNA

A defense system found in animals involves a type of ncRNA called PIWI-interacting RNA

ncRNA interacts with PIWI proteins and inhibits the movement of transposable elements

Blocker

ncRNA physically prevents a cellular process

Decoy

ncRNA recognizes another ncRNA and sequesters it. Acts as a competitor like transcription factors

Originin of replication bacterial chromosomes

oriC. Origin of replication

Merozygotes

partial diploid bacterial cells containing F plasmid carrying some bacterial genes. Useful for investigating whether components of bacterial operons are cis or trans acting factors

When piRISCs directly inhibit RNAs in cytosol

piRISC binds to TE RNA and an argonaute protein within piRISC cuts it into pieces, inactivating it

piRNAs associate with PIWI proteins to form complexes known as

piRNA induced silencing complexes (piRISCs)

General transcription factors

required for the binding of RNA pol to the core promoter and its progression to the elongation stage

Oogenesis

the production, growth, and maturation of an egg, or ovum

The template strand is read in the

3' to 5' direction. The new strand is made 5' to 3'

In DNA methylation, a methyl group is added to

Cytosine residues

In interphase, each chromosome is located in

A distinct chromosome territory

Mutant allele

A less common version of a gene

A eukaryotic chromosome contains

A long, linear DNA molecule

Binding of the lac repressor to two operator sites requires that the DNA form a loop

A loop in the DNA brings the operator sites closer together. Facilitates the binding of the repressor protein

High chi square values indicate

A low probability that the observed deviations are due to random chance alone

Low chi square values indicate

A low probability that the observed deviations are due to random chance alone

Coiling of the shell is controlled by

A maternal effect gene. Phenotypes controlled by the genotype of the mother

Supercoiling in bacteria is controlled primarily by

DNA gyrase and DNA topoisomerase I

Amino acids acetylated in histones

Lysine

Plants have evolved developmental regulatory systems that

Parallel those of animals

Origins of replication in eukaryotes

Several per chromosome

Spliceosome is composed of

Several subunits known as snRNPs

Xist gene is active on

The condensed chromosome in Barr body

Recriprocal cross

Two crosses that differ in which sex carries the trait

Gene conversion

Two different alleles become identical

RF2 recognizes

UAA and UGA

Hybridization in PCR

Base pairs align of complementary DNA

Telocentric

Centromere at end

Antibodies recognize

Epitotes of an antigen

Germ line transformation

Introducing transgenes

microRNA

Made from endogenous genetic material

The trait that is masked in the F1 is

Recessive

Direct repair

Reverse covalent modifications

Mutations can occur at the chromosomal or

Single gene level

Mutations can alter chromosome

Structure

Syntheitc RNA helped decipher

The genetic code

X linked genes

Those on X only

Amino acids altered in nonsense mutation

Many

GFB can be used as

An expression marker, and to study protein localization

Alternate and adjacent 1 segregations are the likely outcomes when

An individual carries a reciprocal translocation. Occur at about the same frequency

Genetic mosaic

An individual that has somatic regions that are genotypically different from each other

Homozygous

An individual with two identical alleles

Genotype

An individual's specific alleleic compositon

Summary of translational initiation

An initiation factor complex binds to the 5' cap in mRNA. The mRNA binds to a complex consisting of the 40S subunit, tRNA met, and other initiation factors. The entire assembly moves along the mRNA scanning for the right start codon. Once it finds the AUG, the 40S subunit binds to it. The 60S subunit joins to from the 80S initiation complex

Translational repressors

Aprotein that binds to mRNA and inhibits its ability to be translated

Extranuclear inheritance is also known as

Cytoplasmic inheritance

miRNAs are an important form of gene regulation

It can silence certain forms of mRNAs

O1 operon operator site for lac repressor

Slightly downstream from the promoter

Submetacentric

Slightly off center

Heterozygous

An individual with two different alleles

Coding strand

Same sequence as the RNA

Intergenic genes

Short regions between adjacent genes

The lac repressor binds to what site within the lac operon

lacO

F2 generation

offspring of the F1 generation

Specific short sequences are critical for promoter sequences

-35 sequence and -10 sequence aslo known as pribnow box

One map unit is equivalent to

1% recombination

Genes are always represent as the DNA sequence of the conding strand

5' to 3' sense strand

Recessive pattern of inheritance: two affected individuals will have

100% affected offspring

Human mtDNA

13 genes that function in oxidative phosphorylation

Autosomal aneuploidies most compatible with survival are trisomies

13, 18, and 21

A binds with T with

2 hydrogen bonds

Allopolyploidy

2 sets of chromosomes, one from each of 2 different species. More common autopolyploidy.

Linkage

2+ genes that do not independently assort because they are physically associated (on the same chromosome)

Linkage groups in humans

22 autosomal linkage groups, one X chromosome linkage group, and one Y chromosome linkage group

Recessive pattern of inheritance: two unaffected heterozygous individuals will on average have

25% affected offspring. Can skip generations

Segmentation genes

3 classes: gap, pair rule, and segment polarity genes. Divide embryo into a series of stripes or segments. Define number, size and polarity of each segment

Trisomy

3 copies of a chromosome (2n+1)

G binds with C with

3 hydrogen bonds

Codons in mRNA

3 nucleotide seqences within the mRNA that specify particular aminos acids

The RNA modification that is important for mRNA stability

3 polyA tailing and 5' prime cap

UvrA, B, C, and D recognize and remove

A short segment of damaged DNA. DNA polymerase and ligase finish the repair job

Random insertion may place an element near a cellular promoter which will produce

A silencing RNA

Hemizygous

A gene present on the X chromosome that is expressed in males in both the recessive and dominant condition

trpR

A gene that encodes the trp repressor protein

Single guide RNA (sgRNA)

A 20 nt region pairs with target DNA. By altering the 20nts, the effector complex can be targeted to different sequences

Heteroduplex

A DNA double helix composed of single strands from two different DNA molecules

Cis effecting or cis acting element

A DNA sequence that must be adjacent to the gene(s) it regulates. DNA sequences that bind regulatory proteins

Homeobox

A DNA sequence within a homeotic gene that regulates development in animals. Encodes a 60 amino acid DNA binding domain

Transposition often occurs around the tme of replication

A TE can transpose ahead of the replication fork and be copied again. One genome will still have one TE, but the other will now have two copies

Maternal effect genes

A gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the genotype

DNA obeys the AT/GC rule of base pairing but during DNA replication an incorrect base may be added by mistake creating

A base pair mismatch

Mutagens

A chemical or physical agent that interacts with DNA and causes a mutation

An inversion

A chromosomal segment that has been flipped to the opposite orientation

A chromosomal deletion occurs when

A chromosome breaks and a fragment is lost

Secondary structure of tRNAs

A cloverleaf pattern containing 3 stem loop structures, variable regions, an acceptor stem with a 3' single stranded region

DNA library

A collection of thousands of different cloned fragments of DNA

Epistatic interactions often arise because two different proteins participate in

A common cellular function. For example an enzymatic pathway

Several human disease have been shown to involve inherited defects in genes involved in NER

A common characteristic is an increased sensitivity to sunlight

Feedback inhibition

A common mechanism to regulate the activity of metabolic enzymes. The final product in a pathway often can inhibit an enzyme that acts early in the pathway

The size and shape of all animal bodies are controlled by

A common set of genes and developmental mechanisms

Homologous recombination

A donor DNA template can be added (with homologous ends to the break) which will be switched into the chromosome. Can be used to add a desired sequence of DNA

RISC is composed of

A double stranded RNA molecule that is 20-25bp long produced from pre-miRNAs and pre-siRNAs by dicer. One strand will be degraded

Many RNA viruses have either dsRNA genome or exist as

A dsRNA during their life cycle

A single chromosome usually has

A few hundred to several thousand genes

Variation in functional activity in overdominance

A gene E encodes a metabolic enzyme

X linked

A gene carried on the X chromosome. If a male inherits an X-linked recessive trait from his mother, he expresses that trait because the Y from his father has no counteracting gene. Females are more likely to be carriers of X-linked traits but are less likely to express them

Inversion position effect

A gene is repositioned in a way that alters its expression

Development biology looks to answer how

A given cell at a precise position in the embryo switches on or off specific genes at timed stages of development

Punnett square

A grid that enables one to predict the outcome of a simple genetic crosses

Operon

A group of two or more genes under the transcriptional control of a single promoter

Viral envelope

A membrane that cloaks the capsid that in turn encloses a viral genome.

One of the strands of DNA serves as a template whose information is transcribed into

A messenger RNA mRNA

Mapping

A method of determining the location of genes relative to each other on the chromosomes

Blotting

A method of transferring RNA/DNA/Proteins onto a membrane

Karyotype

A micrograph of metaphase chromosomes from a cell arranged in standard fashion

Disease resistance in over dominance

A microorganism infects a cell only if cellular proteins function optimally

X linked inheritance

A pattern of inheritance in which a recessive gene is carried on the X chromosome, so that males are more likely to be affected

Prophage

A phage genome that has been inserted into a specific site on the bacterial chromosome.

Testcross

A phenotypically sominant individual is mated with recessive individual

Nucleotide structure

A phosphate group, a pentose sugar (DNA or RNA), a nitrogenous base (A,G,C,T)

When a flower has male and female structures

A plant can fertilize itself, or can be crossed to another different plant

An operon encode

A polycistronic mRNA that contains the coding sequence for two or more genes

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex in bacteria

Attenuator sequence

A segment of DNA important in termination of transcription in attenuation

Genetic transfer

A segment of DNA is transferred from one bacterium to another. Useful for mapping genes

An insulator

A segment of DNA that functions as a boundary between two genes/DNA regions

Gene

A segment of DNA used to make a functional product

Intron

A segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes

A chromosomal translocation occurs when

A segment of one chromosome becomes attached to another

Operator

A sequence of bases that provides a binding site for a repressor protein

Promoter

A sequence of bases that signals the beginning of transcription

A CRISPR array consists of

A series of palindromic sequences separated by spacers derived by foreign DNA molecules (from viruses or plasmids)

Conjugation is mediated by

A sex pilus

Notch signaling pathway

A short range system that works through direct cell-cell contact to control the developmental fate of interacting cells

Mitochondria codons

AUA=methionine, UGA=tryptophan

When PIWI protein is mutated in flies

A transposable element called the P element proliferates and testes are smaller

Lysogenic cycle

A viral reproductive cycle in which the viral DNA is added to the host cell's DNA and is copied along with the host cell's DNA

The start codon for eukaryotic translation is

AUG. Usually the first QUG after the 5' cap

Spontaneous mutations can be caused by

Aberrant recombination, aberrant segregation, errors in DNA replication, transposable elements, depurination, deamination, tautomeric shifts, toxic metabolic products

Aberrant segregation

Abnormal chromosomal segregation may cause aneuploidy or polyploidy

Three types of DNA sequences in oriC are functionally significant

AT-rich region, DnaA boxes, GATC methylation sites

What drives strand separation in bacterial replication

ATP for energy

Typically mitochondrial disease affect cells that require high levels of

ATP for proper functioning

One aspect of mitochondrial diseases is that they have different symptoms but all show deficiencies in

ATP synthesis

Some chemical mutagens disrupt appropriate pairing between nucleotides by

Alkylating bases within the DNA

The different globin gene paralogs

All bind oxygen, myoglobin stores oxygen in muscle cells, different globins in the red blood cells at different developmental stages

Sex chromosome aneuploidies generally have less sever effects explained by X inactivation

All but one X chromosome transcriptionally suppressed

The genes assorted independently

All eight combinations (3 genes, two alleles each) would occur in equal proportions

The genome comprises

All the genetic material that an organism posses

Hox genes are not specific to insects and have been identified in

All vertebrates

Genomic imprinting of the Igf2 gene

Allele from the father is expressed but the mother's is not. Based on patterns of DNA methylation which occurs in two regions near the gene

Sex influenced

Allele is dominant in one sex, but recessive in the other. These genes are on an autosome, not a sex chromosome. Sex is influencing heterozygotes

Allele i is recessive to both IA and IB

Alleles IA and IB are codominant. In cells with both alleles the trait is a combination of both phenotypes

Epistasis

Alleles for one gene masks another (for example, two different proteins combine to provide function)

Variation in function

Alleles may have slight variations in function or in the temperature at which they function

Dominant mutant alleles

Alleles that effect phenotype as just one copy. Less common in natural populations

The lac repressor is inactivated by binding to

Allolactose

Degradative plasmids

Allow bacterium to metabolize an unusual substance

Selectable marker

Allow for isolation of host cells that carry the vector and force them to maintain the vector-usually antibiotic resistance

Transcriptional activators

Allow for switch from initiation to elongation

Fluorescence (emmitance of a specific light frequency)

Allows us to see stuff

Two main types of secondary structures

Alpha helix and beta sheet

One polypeptude can have regions of both

Alpha helix and beta sheet. Other regions may lack secondary structures

Chromosomes are replicated and passed from parent to offspring

Also from cell to cell during development. Chromosomes retain individuality during transmission

Silent mutations

Alter codon but do not change the amino acid encoded

Retroviruses can also move genes in and out of genomes and

Alter host gene expression

5' and 3' untranslated (UTR) region can

Alter stability of RNA and in regulatory element/operator site can get disruption of regulation of gene expression

Missense mutations

Alter the amino acid sequence. Still code for an amino acid, but not the correct amino acid

Transposable elements effects on gene expression and chromosome structure

Altering protein encoding genes, altering or providing new regulatory elements, changing splicing patterns, serving as DNA methylation sites, recombination between transposons can cause chromosomal rearrangements

Remodeling complexes may alter nucleosome structure in several ways

Altering the contact between DNA and histones, altering the path of the DNA around the nucleosome, altering the structure of the nucleosome core itself

Chromatin structure is highly dynamic and it is regulated by

Altering the specific histone proteins present in nucleosomes, modification to histone tails, modifications to the DNA itself (methylation)

Meiotic segregation can occur in one of three ways

Alternate segregation, adjacent 1 segregation, adjacent 2 segregation

One benefit of genes with introns is a phenomenon called

Alternative splicing

Gene regulation via RNA processing and translation

Alternative splicing, RNA stability, RNA interference, translational regulation

Missense mutation

Alters the amino acid sequence

tRNA take the anticodon to produce the

Amino acid

Aminoacyl-tRNA synthetases catalyze a two step reaction involving three different molecules

Amino acid, tRNA, and ATP

tRNA work with the ribosome, read mRNA from 5' to 3', adds amino acids to the polypeptide chain to make

Amino acids

The common stable form of adenine and cytosine is the

Amino form. At a low rate, A and C can interconvert to an imino form

Histone proteins have a globular domain and a flexible charged

Amino terminus or tail

qPCR is used for comparing

Amount of DNA template

Amount of product from qPCR correlates with

Amount of target in sample

Quantitative PCR (qPCR)

Amounts of product produced are measured in real time during the PCR process, not just at the end

PCR basic definition

Amplify the gene of interest

PCR research applications

Amplifying, library screening, genotyping, modifying DNA sequence, differential screening, quantifying gene expression

Retroelements transpose via

An RNA intermediate

Cellular proteins target to a particular location within cells is facilitated by

An RNA protein complex called signal recognition particle (SRP)

Anitsense RNA

An RNA strand complementary to mRNA

RNAs containing 3 nucleotides could stimulate ribosomes to bind a tRNA

An RNA triplet acts like a codon. Different triplets could cause binding of different tRNAs and their associated amino acids

Base excision repair and nucleotide excision repair

An abnormal base is recognized and removed from the DNA and a segment of DNA in this region is excised, and then complementary DNA strand is used as a template to synthesize a normal DNA strand

The lac operon is also regulated by

An active protein. It can be transcriptionally regulated by catabolite repression

Adaptor hypothesis

An adaptor molecule connects the codon and the amino acid

Incomplete penetrance

An allele does not always penetrate into the phenotype of the individual. Not all individuals with a mutant genotype show the mutant phenotype

Sex influenced traits

An allele is dominant in one sex but recessive in the other. Thus sex influence is associated with heterozygotes

Mutations can be detrimental if they result in

An allele that functions more poorly than the original

Lethal allele

An allele that has the potential to cause death. Generally inherited in a recessive manner. Typically mutation in an essential gene

IPTG

An allolactose analogue that can induce the lacZ gene

Missense mutations change a codon and result in

An altered amino acid within a protein coding portion of a gene. Ex: GAC to GAG

Difference between an endonuclease and an exonuclease

An endonuclease can cleave within a strand, whereas an exonuclease digests a strand, one nucleotide at a time

Reverse transcriptase

An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis

Direct repair

An enzyme recognizes an incorrect alteration in DNA structure and directly converts in back to a correct structure

Allele E2 encodes

An enzyme that functions better at higher temperatures

Nonrecombinant

An offspring whose combination of traits has not changed from the parental generation

Example of paralogs: globin genes

Ancestral globin gene has been duplicated and altered. 14 paralogs on three different chromosomes

Variation in chromosome number (of individual chromosomes or sets)

Aneuploidy (individual) eploidy (sets)

Chromosome numbers can vary in two main way

Aneuploidy and euploidy

MADS box proteins

Another DNA binding domain

Maternal effect gene types

Anterior, posterior, terminal group

Segment polarity genes divide each segment into

Anterior-posterior axes, which are then given identity by hox genes

Vectors usually have a gene that confers

Antibiotic resistance. Frequently ampicillin resistance for plasmid vectors

Non coding RNA

Any RNA that doesn't encode a polypeptide. Used in DNA replication, gene regulation, transcription/translation, genome defense

Genetic mapping

Any method used to determine the linear order and relative distance between genes that are linked

An antigen refers to

Any molecule that is recognized by an antibody

Gene regulation can occur at

Any of the points on the pathway to gene expression

Somatic cells

Any other cell that doesn't give rise to gametes. Mutations can be passed on to future generations

The lagging strand is made in short bits in the direction

Away from the replication fork

Chemical mutagen

Base modifiers, intercalating agents, base analogs

Induced mutations chemical mutagens

Base modifiers, intercalating agents, base analogs

DNA protein complex for chromosome compaction

Chromatin

Chemical mutagens come in three main types

Base modifiers, intercalating ages, base analogs

Many factors contribute to the tertiary structure of RNA

Base pairing and base stacking within the RNA, interaction with ions, small molecules and proteins

Competent cells

Bacteria able to take up DNA. Carry genes that encode proteins called competence factors

Nucleoside

Base+sugar

Nucleotide

Base+sugar+phosphate

Restriction enzymes are produced naturally by

Bacteria to protect against foreign DNA (bacteriophages)

ncRNAs preform an array of cellular functions in

Bacteria, archaea, and eukaryotes

CRISPR RNAs are encoded by DNA sequences found in

Bacterial and archael genomes

One origin of replication required to initiate DNA replication in

Bacterial chromosomes

Release in viral reproduction

Bacteriophage cause cell to rupture-lysis. Some eukaryotic viruses bud from cell. Results in an envelope of cellular membrane. Membrane may also have viral proteins

The CRISPR-Cas system provides bacteria with defense against

Bacteriophages

Reciprocal translocations lead to rearrangement of genetic material, not a change in total amount. Thus they are called

Balanced translocations

The inactive X chromosome in a human female somatic cell is called a

Barr body

Ionizing radiation can cause

Base deletions, nick in DNA strands, cross linking, oxidized bases, and chromosomal breaks

DNA polymerases have 3' to 5' proofreading ability that can detect

Base mismatches and fix them. If proofreading fails, the mismatch repair system steps in

By varying annealing conditions sequences with more or less identity can

Be detected

Base analogs

Become incorporated into daughter strand during replication

Some euploidy variations are naturally occurring. Ex: bees

Bees are haplodiploid. Females are diploid and males are monoploid (contain a single set of chromosomes)

Behavioral sex determination

Behavioral interactions can determine sex

Primordial myoglobin

Better at binding and storing oxygen in muscle

Pimordial hemoglobin

Better at binding and transporting oxygen via red blood cells

Many response elements are orientation independent

Bidirectional. Function in the forward or reverse orientation

Inducers function in two ways

Bind activators and cause them to bind to DNA. Bind repressors and prevent them from binding DNA

Inducers function two ways to promote transcription

Bind activators and cause them to bind to DNA. Bind repressors and prevent them from binding to DNA

Corepressors

Bind repressors and cause them to bind to DNA

Initiation relies on the ability of RNA polymerase to

Bind to DNA

Small effector molecules

Bind to activators and repressors. Called inducers, corepressors, or inhibitors

The subunits of spliceosome carry out several functions

Bind to an intron sequence and precisely recognize the intron-exon boundaries. Hold the pre-mRNA in the correct configuration. Catalyze chemical reactions that remove introns and covalently link exons

Three common ways that the function of regulatory transcription factors can be affected

Binding of a small effector molecule, protein-protein interactions, covalent modifications

Translational repressors inhibit translation in two ways

Binding to the shine-dalgarno sequence and/or the start codon (blocks the ribosome from initiating translation). Binding outside the shine-dalgarno/start codon region (stabilize an mRNA secondary structure that prevents initiation)

RF3 doesn't recognize any of the three codons

Binds GTP and helps facilitate termination process

Promoter in lac operon

Binds RNA pol holoenzyme

RNA induced silencing complex (RISC)

Binds pieces, makes them single stranded then uses them to target and break down complementary mRNAs

TFIID general transcription factor

Binds to TATA box. Recruits RNA polymerase

tRNA function

Binds to codons in the mRNA and carries amino acids to the ribosomes to be assembled into a protein.

H1 linker histone

Binds to linker DNA and nucleosomes but not as tightly as the core histones

The lac repressor

Binds to the operator and prevents transcription

Iron regulatory protein (IRP)

Binds to transferrin receptor mRNA and to ferritin mRNA and controls their translation

trp operon is involved in

Biosynthesis of the amino acid trytophan

Repressors sit by the promoter region and

Block transcription

Fetal hemoglobin can cause problems when nitrite pollution irreversibly binds to fetal hemoglobin and causes

Blue baby syndrome

Homeotic selector genes specify

Body parts

A person with IA IB blood type AB

Both alleles are expressed, known as codominance

Different combinations of gene expression specify

Both segment type and order

Smooth and striated muscles produce more tropomysoin mRNA than

Brain cells

DNA double strand breaks are very dangerous

Breakage of chromosomes into pieces caused by ionizing radiation, chemical mutagens and free radicals. Can cause chromosomal rearrangements and deficiencies

Deletion-portion of chromosome is missing. Due to

Breaks in the chromosome that result in loss of fragment

Robertsonian translocation occurs such that

Breaks occur at the extreme ends of two non homologous chromosomes. The small acentric fragments are lost. Larger fragments fuse at centromeric regions to form a single chromosome

DNA helicase

Breaks the H bonds between strands

Need to know the genotype of the parents to

Build a punnett square

X-Gal

Colorless compound that is cleaved by B-galactosidase into a blue dye

ncRNA molecules involved with genome defense

CRISPR RNA, PIWI-interacting RNA

Most widely used system for gene editing

CRISPR-Cas9

DNA amplification occurs in two ways

Cell division and vector replication

Maternal effect genes encode RNA and proteins that play important roles in the early step of embryogenesis

Cell division, cleavage pattern, body axis

Many lethal alles prevent

Cell division. Death at early age

Proteins are the casual participants of

Cell structure and function

When E-cadherin levels are low

Cells can more easily move to new sites in the body

Germ line cells

Cells that are or give rise to gametes. Mutation is heritable

Recombinant cells

Cells that contain new allelic combination

In intergenic suppressor, proteins may act in the same

Cellular pathway

Bacteria often posses allelic differences that affec their

Cellular traits

Paracentric inversion

Centromere is outside inverted region

Pericentric inversion

Centromere is within inverted region

Acrocentric

Centromere more off center

Metacentric

Centromere near the middle

Submetacentric

Centromere slightly off center

Probability of an outcome is the

Chance or likelihood that the outcome will occur

Reverse mutation

Change a mutant alleles back to wild type

Mutation

Change in DNA sequence

Mutation

Change in DNA sequences (bases)

Position effect

Change in expression of a gene associated with a change in the gene's location within the genome

Inversion

Change in the direction of part of the chromosome. Chromosomal segment has been flipped to the opposite orientation. Amount of genetic info does not change

Chromosome structure alteration: inversion

Change in the direction of part of the genetic material along a single chromosome

Forward mutation

Change in wild type genotype to something new

Transversion

Change of a purine to a pyrimidine or vice versa

Transition

Change of purine to purine or pyrimidine to pyrimidine

A reverse mutation or reversion

Changes a mutant allele back to the wild type

Nonsense mutation

Changes codon into a stop codon

Nonsense mutation

Changes codon to stop codon

As cells enter metaphase, the level of compaction

Changes dramatically

Oxidative DNA damage

Changes in DNA structure that are caused by reactive oxygen species (ROS) if they're not removed

Maternal inheritance in

Chloroplast (cpDNA) and mitochondria (mtDNA)

CRISPR

Clustered regularly interspaced short palindromic repeats

TFIID requires

Coactivators

RNA splicing

Coding sequences in DNA called exons are interrupted by intervening sequences or introns. Transcription copies the entire gene product and introns are later removed, exons are connected together or spliced

mRNA involved in protein synthesis

Coding template

A heterozygote has a phenotype where the contribution of both alleles is evident

Codominance

The genetic information is coded within mRNA in groups of three nucleotides known as

Codons

Many but not all species of bacteria can

Cojugate

RNA induced silencing complex (RISC)

Combination of a small interfering RNA (siRNA) molecule or a microRNA (miRNA) molecule and proteins that can cleave mRNA, leading to the degradation of the mRNA, or affecting transcription, or repressing translation of the mRNA

2D electrophoresis

Combine IEF then SDS-page2 for max separation. Can identify protein spots by mass spectrometry

To fit bacterial cells, the chromosomal DNA must be

Compacted 1000 fold. Proteins organize the DNA into loops

Negative supercoiling helps

Compaction of the chromosome and creates tension that may be released by DNA strand separation

The nuclear matrix

Compacts DNA into radial loop domains. Composed of two parts: nuclear lamina and internal nuclear matrix

Synteny

Comparison of gene order within two sets of chromosomes

cDNA

Complementary DNA. DNA produced synthetically by reverse trascribing mRNA

During mRNA-tRNA recognition the anticodon in tRNA binds to a

Complementary codon in mRNA

All RNAs originate as

Complementary copies of one of the two strands of DNA

The template strand is used to make

Complementary copy of RNA

Non coding strand (template)

Complementary sequence

Anti-miRNA oligonucleotides (AMOs)

Complementary to a specific miRNA and base pairs with it. Blocks the ability of miRNA to function and/or cause it to be degraded

Oligonucleotide primers in PCR

Complementary to sequences at the ends of the DNA fragment to be amplified. Synthetic and about 15-20 nucleotides long. Need to know sequence of DNA to be bound by primers

A phenomenon in which two different parents that express the same or similar recessive phenotypes produce offspring with a wild type phenotype

Complementation

Compaction of interphase chromosomes is not

Completely uniform

The piRISCs enter nucleus and bind to RNA molecules being transcribed from TEs then

Complex then direct the methylation of DNA and trimethyaltion of lysine 9 on histone H3. Modifications recruit proteins that convert euchromatin to heterochromatin, preventing transcription

cDNA library

Composed of cDNA inserts. Should represent all of the mRNA in the cell

Some proteins function as homodimers

Composed of two subunits. When two polypeptides encoded by the same gene bind to each other to form a dimer

Inheritance patterns that deviate from Mendels law are seen when there is more than one gene that

Controls a single trait

qPCR

Computer monitors the amount of PCR product being made over the course of the reaction via probes

Trisomy 21

Condition in which an individual has three number 21 chromosomes, resulting in Down syndrome. Improper chromosome nondisjunction

Transfer of genetic material from one bacterium to another can occur by one of three mechanisms

Conjugation, transduction, transformation

Internal nuclear matrix

Connects to lamina, fills the nucleus interior

Locked nucleic acids (LNAs)

Contain a ribose sugar that has an extra bridge connecting the 2' oxygen and 4' carbon

Histone proteins are basic

Contain many postively charged amino acids. Lysine and arginine

Probe in southern blot

Contains the DNA and tag that shows all the parts of DNA that are complementary. Using X-rays or fluorescent

Regulation of gene expression primarily occurs at the transcription level but

Control also occurs at other levels before and after translation

Mechanism of HOTAIR transcriptional repression

Creates loops and brings in PRC2 and LSD1 which demethylates lysine on histones to modify methylation patterns in the chromatin around the genes and reduce expression of the gene in that air

DNA gyrase (topoisomerase II)

Creates negative supercoild using energy from ATP. Can also relax positive supercoils when they occur

Parts of CRISPR cas systems

Crispr gene has a group of clustered, regularly interspaced, short, palindromic repeats

Steps for recombinant analysis

Cross two true breeding strains (different in two traits), testcross F1 with a true breeding homozygous recessive indivdual, collect data on F2 generation, collect the map distance between pairs of genes, construct the map

Strategy for using three factor crosses to map genes

Cross two true-breeding strains that differ with regard to the three genes to get offspring that are heterozygous for all genes, mate the F1 female heteros with the male homos recessive for all three

Single factor or monohybrid crosses

Crossed only two variants of one character at a time

Bacteria reproduces asexually

Crosses are not used in the genetic analysis of bacterial species

Two factor crosses

Crossing individual plants that differ in two characteristics

Genes that are far apart on the same chromosome may assort independently from each other and separate by

Crossing over

Genetic duplications are usually caused by

Crossing over between improperly aligned homologous chromosomes

Likelihood of crossing over depends on the distance between the two genes

Crossing over is more likely to occur between two genes that are far apart

Mitotic recombination

Crossing over that occurs during mitosis and produces a pair of recombinant chromosomes. Rare and may produce a pair of recombinant chromosomes that have a new combination of alleles

Linked genes can still independently assort due to

Crossing over where there is recombination between homologous chromosomes during meiosis

Inversion heterozygotes have a high change of producing abnormal gametes due to

Crossing over-inverted segment in inversion loop=abnormal chromosome

Chrloroplasts originated from

Cyanobacterium

The small effector molecule in catabolite repression

Cyclic AMP (cAMP)

Short interfering RNAs are produced by two molecular machines

DICER and RISC

DNA polymerase I excises the RNA primers and fills in with

DNA

Order of eukaryotic chromosomal compaction

DNA alone, nucleosome, 30nm fiber, radial loop domains, compaction of radial loops, metaphase chromosome

Both mitochondria and chloroplasts contain their own

DNA and are inherited through maternal cytoplasm in most organisms

Epigenetic changes can be inherited, but may not follow mendelian inheritance

DNA and chromosomal modifications can occur during gametogenesis or early development

Chromosomes composed of

DNA and protein. Double helix of DNA interacts with proteins resulting in complex structures in the form of chromosomes

The compaction of linear DNA in eukaryotic chromosomes involves interactions between

DNA and various proteins

Illumina sequencing (break down)

DNA binds to flow cell and there are fluorescent bound bases and add just one base. Terminate. Take a picture, wash terminator and add another base

Staggered ends

DNA cleaved creates short single stranded ends or sticky ends. Ends can only be joined to ends with complementary sequences

Blunt ends

DNA cleaved has no single stranded ends, any blunt end can be joined to any other blunt end

C-value=

DNA content in a genome (in picograms)

Difference betwewen DNA and RNA

DNA doesn't have a hydroxyl group on 2' and RNA does. DNA is missing that O

Acquisition is CRISPR-Cas

DNA entering cell is identified, processed and inserted into CRISPR array as a new spacer

In bacteria RNA primers are removed by

DNA pol I

Topoisomerase II

DNA gyrase. Relaxes supercoiling in front of DNA helicase

Mediym and large RNAs involved in

DNA imprinting, X inactivation, DNA demethylation, gene transcription, generation of other RNA classes

Unlike gene cloning PCR copies

DNA in vitro without vectors or host cells

DNA pol I cannot join the small DNA fragments on lagging strand. It's accomplished by

DNA ligase

Different molecular changes can underline epigenetic phenomena

DNA methylation, chromatin remodeling, covalent histone modification, localization of histone variants, feedback loops

DNA methylation is carried out by

DNA methyltransferase

Gene conversion occurs in one of two ways

DNA mismatch repair or DNA gap repair synthesis

Base excision repair involves a category of enzymes known as

DNA n-glycosylases. These can recognize an abnormal base and cleave the bond between it and the sugar in the DNA. AP endonuclease then make a cut on the 5' side

Virus chromosomes consist of single or double stranded

DNA or RNA

Matrix attachment regions AKA scaffold attachment regions

DNA sequences interspersed in the genome. They anchor to the nuclear matrix, forming radial loops

SMART sequencing

DNA strand and a single polymerase linked to the bottom of the DNA. The cell is loaded with the four nucleotides incorporated with fluorescence. So there is a flash of light every time a base is added (different color for each)

DNA replication summary

DNA strands come apart, each serves as a template for synthesis of new strands

Vector DNA

DNA that can replicate within an organism without integrating into a host chromosome-plasmids and viruses. Serves as the carrier of the DNA segment to be cloned

Nucleosome remodelers have

DNA translocases. they can move along DNA

Mendels law of independent assortment

During gamete formation, the segregation of any pair of hereditary determinants (alleles) is independent of the segregation of other pairs (alleles of other genes). Two different genes randomly assort their alleles during the formation of haploid cells

Alternative splicig allows one gene to

Encode more polypeptides

lacZ

Encodes Beta galactosidase. Cleaves lactose and lactose analogues. Also convers lactose in allolactose (an isomer)

i alleles in ABO blood type

Encodes a defective enzyme that can't add sugars. The carbohydrate tree is short (called H antigen)

Genes not in the nucleus like in extranuclear inheritance become part of the cell by

Endosymbiosis

Activator proteins bind to what type of DNA sequence?

Enhancers

Beneficial mutation

Enhances survival or reproductive success

A beneficial mutation

Enhances the survival or reproductive success. Good for evolution

piRISCS can prevent transposable element movement in two ways

Enter nucleus and bind to RNA molecules being transcribed from TEs or directly inhibit RNAs in cytosol

Random mutation hypothesis

Environmental factors simply select for the survival of individuals with beneficial mutations

To make synthetic RNA they used

Enzyme polynucleotide phosphylase. In the presence of excess ribonucleoside diposhphates (NDPs) it catalyzes covalent linkage of ribonucleotides into RNA

DICER

Enzyme that cleaves and processes double stranded RNA to produce siRNAs or miRNAs that are 2o-25 nucleotids in length

Integrase

Enzyme that mediates integration

DNA methyltransferase

Enzyme which attaches a methyl group to the number 5 position of the cytosine base, forming 5-methylcytosine

DNA polymerases

Enzymes that catalyze formation of the phosphodiester bond between nucleotides. Synthesize the DNA molecule

Restriction enzymes (endonucleases)

Enzymes that cut DNA at a specific sequence

A cross involving a two gene interaction can produce two distinct phenotypes due to

Epistasis

An inheritance pattern in which the alleles of one gene mask the phenotypic effects of the alleles of a different gene

Epistasis

A key aspect of TRNE is that the triplet repeat can form a hairpin (or stem loop) leading to

Errors in DNA replication

Destabilizing elements are found

Especially in mRNAs that have short half lives. Can be found anywhere on the mRNA

Imprinting can be divided into three stages

Establishment of imprint during gametogenesis, maintenance of the imprint during embryogenesis and in the adult somatic cells, erasure and reestablishment of the imprint in the germ cells

RNA splicing is common in

Eukaryotes and occurs occasionally in bacteria

mRNA processing

Eukaryotic mRNA is modified before it leaves the nucleus. Spliced, capped at 5' end. Poly-A addition at 3' end

The twist demonstrates a non mendelian pattern of inheritance

Even though twist is controlled by a nuclear gene

Mutations are the foundation for

Evolutionary change

Mutations can be harmful and as a result organisms have

Evolved ways to repair damaged DNA

Many genes have multiple alleles (three or more)

Ex: ABO blood type genes in humans

Temperature sensitive (ts) lethals

Ex: a developing drosophila larva may be killed at 30C but will survive if grown at 22C

Some cellular proteins must be targeted to a particular location within cells

Ex: extracellular proteins must be targeted to the plasma membrane in bacteria or to the ER to be secreted

Some lethal alleles exert their effect later in life

Ex: huntingtons disease. Progressive degeneration of nervous system, dementia and early death

Environmental conditions may have a great impact on phenotype

Ex: the arctic fox changes coat color from grayish brown in summer to white in winter

The coding strand has the same base sequence as the RNA transcript on the template strand

Except U instead of T

Illegitimate recombination

Exchange of genetic information between non-homologous DNA molecules

Capping is added to the 5' end of the RNA for

Export from nucleus

Regulated gene expression

Expression may be increased or decreased according to the demand for the gene expression. Encoded proteins will be produced only when required

miR-200 miRNAs are associated with a decrease in

Expression of E-cadherin, a membrane protein that adheres adjacent cells together

Phenotypes of X chromosome aneuploidies may be due to

Expression of X linked genes prior to X inactivation and imbalance in expression of pseudoautosomal genes

Fertility plasmids

F factors that allow conjugation

Strains of bacteria that contain the F factor are designated

F+ and those lacking are F-

The F factor carries genes that allow for transfer of DNA from

F+ cell to F- cell

Sex pili are made only by

F+ strains. They act as attachment sites for other bacteria

For all 7 characters studied

F1 generation showed only one of the two parental traits and F2 generation showed a 3:1 ratio of the two parental traits

Competent cell function

Facilitate binding, uptake and subsequent incorporation of the DNA into the bacterial chromosome

Blending hypothesis

Factors that control hereditary traits are malleable. Blend together generation after generation

Down syndrome

Failure of chromosome 21 to segregate properly due to chromosomal nondisjunction, usually in meiosis I in the oocyte

Meiotic nondisjunction

Failure of chromosomes to segregate properly during anaphase of meisosis. Results in mosaic

Ion torrent

Flushes curvet with each base individually. Measures change in pH. The change in pH tells which base is each. Slower but less expensive

Transfer RNAs tRNAs

Fold into basically the same shape as RNA but they have different sequences

A protein that is a repressor for one gene may be an activator

For another protein

Limit to length of fragment that can be amplified

For most commercial enzymes a few kb. Improved enzymes are constantly being developed

Promoter in eukaryotes

For protein encoding genes, the core promoter often consists of a TATA box and a transcriptional start site

Chromatin remodeling

For replication and gene expression, chromatin must relax its compact structure and expose regions of DNA to regulatory DNA binding proteins

During meiosis I, homologous chromosomes synapse with each other

For the translocated chromosome to synapse properly, a translocation cross must form

Short interfering RNAs (siRNAs)

Form dsRNA. Can be exogenous from a virus or from a researcher wanting to study gene function

Moderately repetitive DNA sequence

Found a few hundred to a few thousand times. Includes genes for rRNA and histones, origins of replication, and transposable elements

Z-W sex determination

Found in birds and some fish. Male is Z-Z the homogametic sex and the females is Z-W the heterogametic sex

X-0 sex determination

Found in many insects, such as grasshoppers. Male is X-0 (has just one X chromosomes). Female is XX

Selenocysteine the 21st amino acid

Found in several enzymes of redox reactions. Encoded by UGA (normally a stop)

Pyrrolysine the 22nd amino acid

Found in some methane producing archaea. Encoded by UAG (normally a stop)

Pseudoautosomal genes

Found on both X and Y. Inheritance patterns are similar to autosomal gnes

Unique or non-repetitive DNA sequence

Found once or a few times in the genome, includes structural genes as well as introns and other noncoding DNA

Highly repetitive DNA sequence

Found tens of thousands to millions of times. Each copy is relatively short

Different patterns of expression of a set of genes called homeotic genes (hox)

From wide range of organisms have a common ancestry

Disease resistance: A microorganism infects a cell only if cellular proteins

Function optimally

A second antibody binds to the first antibody

Fused to a enzyme that creates a visible product

Giemsa stain

G bands. Produces characteristic patterns on DNA

Maternal effect

Gene expression in the mother determines traits of offspring. Genotype of father and offspring has not effect. Controlled by nuclear genes

Mutations in noncoding sequences can affect

Gene expression. But will most likely not do anything

Duchenne muscular dystrophy (DMD)

Gene for DMD i s on the X chromosome. Encodes dystrophin protein, needed muscle structure. Dames heat and breathing muscles

Pleiotropic effects occur because

Gene product may affect cell function in multiple ways, gene may be expressed in different cell types, gene may be expressed at different stages of development

A pattern in which the loss of function in a single gene has no phenotypic effect, but the loss of function of two genes has an effect. Functionality of only one of the two genes is necessary for a normal phenotype

Gene redundancy

Highly condensed metaphase chromosomes undergo little

Gene transcription

The ultimate action of a steroid hormone is to affect

Gene transcription

Homolog

General term for genes that share similar sequence

Two types of transcription factors in eukaryotes

General transcription factors and regulatory transcription factors

P elements are also being used to

Generate mutations and to clone mutant genes

Reactive oxygen species (ROS)

Generated by normal metabolism. Used by immune system to kill invading cells

Transcriptional networks regulate development by

Generating patterns of gene expression. Working in a cascade.

Epigenetic inheritance and imprinting

Genes are altered in the offspring (ex methylation)

Genomic pros and cons

Genes in 1:1 ration. Clones have promoters and introns. Huge amount of extra non coding material

Ortholog

Genes in different species that evolved from a common ancestral gene by speciation

Essential genes

Genes required for survival. Absence of the protein product leads to a lethal phenotype

Duplication events can create paralogs

Genes that are similar to one another that are members of a gene family

Segregation analysis is used in conventional plant breeding and used to identify

Genes that control particular traits

Viral and bacterial chromosomes usually only have one

Genome but can have multiple copies

Maternal effect (maternal inheritance)

Genotype of the mother will determine the phenotype of the offspring. Due to accumulation of gene products that the mother provides to her developing eggs

Typically temperature sensitive proteins mis fold at

Higher temperatures, becoming nonfunctional

Geneticists classify animal cells into two types

Germ line cells and somatic cells

Mutations can occur anywhere

Germ line or somatic cells

ABO blood type genes in humans

Glycosyl transferase adds sugars to the carbohydrate tree on the surface of red blood cells. Antibodies can distinguish between cells with different sugars added (between the different antigens)

Chromosomes can only be microscopically visualized at this part of the cell cycle

Going though metaphase, condensed dividing chromosomes

Mitochondria originated from

Gram negative non sulfur purple bacteria. The intracellular bacterial cells evolved to become modern organelles

Looking at pairs of traits for the flies, the more common recombinants (the two traits together)

Greater distance and more crossing over between these genes

Three different splicing mechanisms

Group I intron splicing, group II intron splicing, spliceosome

Retrovirus

Group of RNA viruses which insert a DNA copy of their genome into the host cell in order to replicate. Ex HIV

Kinetochore proteins

Group of proteins that link centromere to spindle apparatus

Exceptions to chloroplasts having maternal inheritance

Gymnosperms have paternal, some angiosperms have biparental

Accessory enzymes

Gyrases, helicases, ligases

The five types of histones

H2A, H2B, H3, H4. Core histones

Five standard histone genes

HI, H2A, H2B, H3, H4

ncRNA molecules involved with chromatin structure and transcription

HOTAIR, COLDAIR, Xist RNA

ncRNAs and changes to chromatin structure

HOX transcript antisense intergenic RNA (HOTAIR)

During gamete formation, the paired factors segregate randomly

Half of the gametes receive one factor and half receive the other

Antagomirs

Have one or more base modification that promotes stronger binding to complementary miRNAs

If a crossover occurs within the inversion loop

Highly abnormal chromosomes are produced

What's important for unwinding the DNA double helix

Helicase, topoisomerase, and single strand binding protein

Some regions of X and Y without genes share homology

Help in pairing X and Y chromosomes during meiosis I

The ability of gyrase to introduce negative supercoils into DNA is crucial for bacteria to survive

Hence this enzyme can be targeted to cure bacterial diseases

Gene mutations

Hertiable changes in gene sequence

Incomplete dominance

Heterozygotes exhibit a phenotype intermediate between the phenotypes of the homozygotes

Incomplete dominance

Heterozygous have an intermediate phenotype

Overdominance

Heterozygous individual has greater reproductive success compared to either homozygous

P elements can insert themselves into or near genes, causing

High rates of mutation

Paralogs

Homologous genes within a single species

Nuclei of most eukaryotic cells contain chromosomes in

Homologous pairs. They are diploid. Gametes are haploid

DNA double strand breaks can be repaired by two systems

Homologous recombination (HRR) and non-homologous end joining (NHEJ)

Repeats in crispr

Homologous to bacteriophage

Steps of action of glucocorticoids

Hormones diffuse through plasma membrane, binds to receptors, a nuclear localization signal is exposed, two receptors dimerize and enter the nucleus, the dimer binds to glucocorticoid response element, this activates trancription

A successful asexual allopolyploid

Horsetails

CpG islands are unmethylated in

Housekeeping genes. Genes that tend to be expressed in most cells

Analysis of developmental mechanisms

How adult body plan is laid down in the embryo, program of gene expression that turns undifferentiated cells into differentiated cells, role of cell cell communication in development

Variable expressivity

How affected an individual may be by a mutation. Ex: a person with an extra toe is said to have low expressivity of polydactyly and a person with several extra is said to have a high expressivity

Whether a trait is dominant or incompletely dominant may depend on

How closely the trait is examined. Mendel concluded that RR and Rr produced round but microscopic examination of round peas revealed that not all round peas are the same

Leader peptide transcript has several trp codons

How fast it is translated depends on how much trp is in the cell. Which hairpins form controls transcription of the rest of the operon

Chromosomes are linkage groups

How strong the linkage is depends largely on how close the genes are on a chromosome

TFIID is a general transcription factor

It binds the TATA box and recruits RNA pol II to the core promoter

Explansion of trinucleotide repeats may be within the noncoding sequence of the gene

Hypothesized to cause abnormal changes in RNA structure. May produce methylated CpG islands to silence the gene

The initiona of translation requires three initiation factors

IF1, IF2, and IF3

Iron response element (IRE)

IRE is found in the 5' UTR in ferritin mRNA. IRE is found in the 3' UTR in transferrin receptor mRNA

Long terminal repeats

Identical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA

Bacterial conjugation methods were sued to introduce different parts of the lac operon mutant into different strains

Identified F factors that carried parts of the lac operon. Bacteria that receive have to copies of the lacI gene one on the chromosome and the other on the F factor

Penetrance is described at the population level

If 60% of heterozygotes carrying a dominant allele exhibit the trait, the trait is 60% penetrant

Western (protein) blotting can determine

If a protein is made in a particular cell type and if a protein is made at a particular stage of development

RNA northern blotting can determine

If a specific gene is transcribed in a particular cell type and if a specific gene is transcribed at a particular stage of development

Genetic mapping is produced by recombination analysis

If the genes are far apart leads to many recombinant offspring. If the genes are close leads to very few recombinant offspring

Oxidative stress

Imbalance between synthesis/destruction of reactive oxygen species

Amino form tautomeric shift

Imino form (gain H) A and C

PolyA tail

Important for mRNA stability, the exit of mRNA from the nucleus, and in the synthesis of polypeptides

Mitotic nondisjunction

Improper sister chromatid separation that leads to trisomic and monosomic daughter cells. Occurs after fertilization. Usually only a subset of cells affected causing mosaicism

Temperature dependent sex determination is found in some reptiles and some fish

In alligators, eggs incubated at 33 degrees grow into males and few degrees they grow into females. The male and female have the same chromosome composition

TEs offer an advantage

In bacteria, may carry antibiotic resistance genes. May cause insertion of exons into the coding regions of other genes, providing new functions

Like chloroplasts, mitochondria are usually, but not always

Inherited from the female parent via egg cells

Linkage is the tendency of genes that are near one another to be

Inherited with one another

In some cases presence a small effector molecule may

Inhibit transcription

Outcomes of RISC binding to mRNA

Inhibit translation without degrading the mRNA. RISC-mRNA complex may remain in a cellular structure called a processing body. Degradation of the mRNA through cleavage by argonaute

miR-200 miRNA act as tumor suppressors by

Inhibiting an event called the epithelial-mesenchymal transition-the initiating step of metastasis

Double stranded RNA is more potent than antisense RNA at

Inhibiting mRNA

DNA replication occurs in three stages

Initiation, elongation, termination

Three stages of transcription

Initiation, elongation, termination

Three phases for X inactivation

Initiation, spreading, maintenance

Frameshift mutation

Insertion/deletion of nucleotides that cause a shift in the reading frame

Genomic imprinting is permanent in the somatic cells of one animal but

It can be altered from generation to generation

Third step of gene cloning

Introduce recombinant vector with chromosomal DNA into host bacteria (transformation if plasmid vector used, stransfection if a viral vector is used)

cDNA lacks

Introns. Useful for expression in prokaryotes

Changes in chromosome structure

Inversions, translocations, duplications, deletions

Transposase recognizes

Inverted repeats at the ends of a transposable element and brings them closer together

Adjacent 2 segregation

Inviable and unbalanced. Adjacent homologous chromosomes segregate into the same cell. Both have duplications and deletions

Adjacent 1 segregation

Inviable and unbalanced. Adjacent non homologous chromosomes segregate into the same cell. Both have duplications/deletions

Frameshift mutations

Involve addition or deletion of nucleotides in multiple of 1 or 2 but not 3 (the size of one codon)

Antisene RNAs, micro RNAs and short interfering RNA functional role

Involved in gene regulation

The tole of snRNPs in the splicing process

Involved in recognizing the intron boundaries, cutting out the intron, and connecting the two adjacent exons together

DNA methylation in eukaryotes

Involves addition of methyl group to cytosine. Occurs most often on cytosine bases after the CpG island

Induced mutations physical mutagens

Ionizing radiation and nonionizing radiation

Physical mutagen

Ionizing radiation and nonionizing radiation

Physical mutagens come in two main types

Ionizing radiation and nonionizing radiation

DNA repair is a multi step process

Irregularity in DNA structure is detected, abnormal DNA is removed, normal DNA is synthesized

During attenuation, transcription begins but

Is terminated before the entire mRNA is terminated

In trinucleotide repeat expansion, the length of a trinucleotide repeat increases above a certain critical size

It becomes prone to frequent expansion

Within the cell the protein will not be found in a linear state

It will adopt a compact 3D structure. This folding can begin during translation

A chromosomal rearrangement may affect a gene that's left intact but

Its expression may be altered because of its new location - called position effect

Restriction sites for

Joining vector DNA to DNA segment to be cloned

Nonhomologous end joining

Joins without template, tends to produce small insertions or deletions, knocks out genes by disrupting reading frames

Promoter location

Just before, or upstream, of where transcription of a gene actually begins

Primers on the leading strand

Just one primer is made

Chromosomal changes in structure or number are generally detected by

Karyotyping: affect more than one gene

Single stranded binding proteins

Keep the two strands separated until after they are copied

Single stranded DNA binding proteins

Keeps strands apart

Single strand binding protein

Keeps the separated strands apart in DNA replication

The common stable form of thymine and guanine is the

Keto form. At a low rate, T and G can interconvert to an enol form

Many lethal alleles prevent cell division

Kill an organism at an early age

Conditional lethal alleles

Kill an organism only under certain environmental conditions

Semi-lethal alleles

Kill some individuals in a population, not all of them. Environmental factors and other genes may help prevent the detrimental effects of semi lethal genes

Genes in the lac operon are involved in

Lactose metabolism

Okazaki fragments

Lagging strand synthesized as many short RNA-DNA molecules

ncRNAs are broadly categorized according to

Length

Factors that can affect mRNA stability include

Length of the polyA tail and destabilizing elements

Euchromatin

Less condense (acetylated)

Euchromatin

Less condensed regions of chromosomes, transcriptionally active, regions where 30nm fiber forms radial loop domains

Non LTR retrotransposons

Less like retrovirus, may encode reverse transcriptase/endonuclease

Small regulatory RNAs (short ncRNAs)

Less than 200 nucleotides

Genetic linkage can be used to make

Linkage maps

Macromolecules

Lipids, carbohydrates, proteins, nucleic acids (DNA and RNA)

PiCDPK1-GFP

Localizes to the plasma membrane and cytosol and acuses loss of growth polarity in pollen tubes. Possesses N-terminal lipid modification sites

Gene location is eukaryotes

Located between the centromeric and telomeric regions along the entire chromosome

Cis acting elements

Located on the same DNA strand. DNA sequences that exert effects only over a particular gene

Inversion breakpoints

Location of breaks leading to inversion occur in a vital gene. Will disrupt gene function

Some AMOs contain chemical modifications that cause them to bind more tightly

Locked nucleic acids and antagomirs

Environmental agents can cause

Long lasting epigenetic changes

In higher eukaryotes genes are

Longer and tend to have many introns

Heterogametic sex

Male that is X-Y. Two kinds of sperm are produced, either X or Y plus 22 autosomes

During the evolution of mitochondria and chloroplasts, most genes have been

Lost or transferred to the nucleus. Gene transfer has been mostly unidirectional from the organelles to the nucleus

Presence of repressor protein does not completely inhibit transcription

Low basal level of transcription. Produces enough Beta galactosidase and permease to sense if lactose is in the environment

Which regions form loops depends on how much trp is in the cell

Low trp: region 2 and 3 form. High trp: region 1 and 2 form, 3 and 4 aslo form and act as a transcriptional terminator

Hypothesis for imprinting

Males want their offspring to have rapid growth and females must balance rapid growth with saving resources for herself and future offspring

Amino acids altered in frameshift mutation

Many

DNA replication licensing

MCM helicase binds, completing a process called

Small interfering RNA

Made from exogenous genetic material. Naturally from viruses. Used by cell to prevent viral infection

MicroRNAs fall under small regulatory RNAs (short ncRNAs)

Majority associated with gene regulation. 20-25 nucleotides

A1A2 heterozygotes

Make A1A1, A2A2, A1A2 homodimers. For some proteins, the A1A2 homodimer may have better functional activity

A1A2 heterozygotes

Make A1A1, A2A2, and A1A3 homodimers. For some proteins, the A1A2 homodimer may be better functional activity

Reverse transcriptase uses RNA as a template to

Make a complementary strand of DNA

Prototrophs

Make all their nutrients from basic components

The goal of DNA replication is to

Make an exact copy of the DNA

A1A1 homozygotes

Make only A1A1 homodimers

A2A2 homozygotes

Make only A2A2 homodimers

In interference phase, cas9 protein function as an endonuclease that

Makes double stranded breaks in the bacteriophage DNA. Phage proliferation is inhibited

Bacteria are usually haploid

Makes it easier to identify loss of function mutations than in Eukaryotas. Recessive mutations are not masked by dominant alleles

Translation RNA

Making polypeptide chains (proteins), composed of amino acids. All from mRNA that came from DNA

Within genes, a linear sequence of deoxyribonucleotides in DNA contains the information for

Making proteins

The sickle cell allele is found at a fairly high frequency in parts of Africa where

Malaria is found

The genetic code is degenerate

Many amino acids specified by more than one codon

Morphological traits such as height, weight, and pigmentation are affected by

Many different genes in combination with environmental factors

Important genes line on the X chromosome

Many of these genes encode proteins that interact with proteins encoded by autosomal genes

If the genes are far apart

Many recombinant offspring

AU rich element (ARE) is found in

Many short lived RNAs

Low levels of miR-200 family of miRNAs have been associated with

Many types of cancer

Three factor crosses can yield information about

Map distance and gene order

Units of distance between genes

Map units or centiMorgans

Linkage maps

Maps of the relative locations, or loci, of genes on a chromosome

Two different sets of genes control embryonic development in drosphila

Maternal effect genes and zygotic genes

Two sets of genes control developmental genetics in animals

Maternal effect genes and zygotic genes

Pigmentation inheritance exhibits a

Maternal inheritance pattern. Depends solely on mother's phenotype because the egg provides the cytoplasm

Nuclei arrange themselves around the periphery of the zygote and are exposed to gradients of

Maternally derived mRNA transcripts and proteins (provide positional information

Single factor cross

Matings look at one character

Two factor cross

Matings look at two characters

Pre mRNA with multiple introns can be spliced different ways generating

Mature mRNAs with different combinations of exons

Sometimes DNA that enters the cell is not homologous to any genes on the chromosome

May be incorporated at a random site on the chromosome this process is termed nonhomologous or illegitimate recombination

Individuals with inversion heterozygotes

May be phenotypically normal but have a high probability of producing abnormal gametes due to crossing over in the inverted segment

Copia elements

May move to different chromosome locations throughout the genome. Ex: variations in eye color and segment formation are due to copia insertions within genes

RNA interference (RNAi)

Mechanism in which double stranded RNA silences mRNA

Mediator function

Mediates interactions between RNA pol II and various regulatory transcription factors

The third component for transcription is a large protein complex

Mediator

Crossing over occurs in

Meiosis I. Exchange of DNA between non sister chromatids of homologous chromosomes results in genetic recombination

Telomeric sequences consist of

Moderately repetitive tandem arrays, 3' overhang that is 12-16 nucleotides long, each species has a variation of the sequence

Genomic imprinting

Modification of a nuclear gene that alters its expression, but is not permanent over the course of many generations. Form of epigenetic inheritance

Small RNAs (snaRNAs, smRNAs, piRNAs) involved in

Modification of target RNAs, synthesis of telomeric DNA, chromatin structure dynamics, transcription modulation, structural role, gametogenesis

Epigenetic inheritance

Modification to a gene that changes gene expression, but is not permanent over the course of generations. May permanently affect the life of an individual. Not a change in the DNA sequence itself

The histone code

Modifications to histone tails. Also called transcription

In addition to the normal A, U, G, C nucleotides, tRNAs commonly contain

Modified nucleotides

A phenomenon in which an allele of one gene modifies the phenotypic outcome of the alleles of a different gene

Modifying genes

Nucleotide excision repair is found in all eukaryotes and prokaryotes

Molecular mechanism best understood in prokaryotes

The relationship between genes and traits spans four level of biological organization

Molecular, cellular, organism, population

Recombinant DNA molecules

Molecules made by joining DNA from two different sources

Low stringency

More dissimilar sequences can hybridize

Polar and charged amino acids are hydrophilic

More likely to be on the surface of a protein

Acrocentric

More off center

Amount of all genes that are protein encoding genes producing mRNA which is translated

More than 90%

The total amount of DNA in eukaryotic species is typically

More than that in bacterial cells

Capping

Most mature mRNAs have 7-methyl guanosine covalently attached at theur 5' end

Monoecious plants

Most plants produce both male and female gametes from the same individual

Sex influenced does not mean sex linked

Most sex influenced traits are autosomal

Each species of organism contains thousands of genes but

Most species have at most a few dozen chromosomes

Human mitochondrial diseases can be transmitted from

Mother to offspring via the egg. Follow a strict maternal inheritance pattern

Paternally imprinted

Mother's allele is expressed

Two common reasons for position effects

Movement to a position near regulatory sequences and movement to a heterochromatic region

The cascade

Multiple cis elemetns regulate each genes as they are bound by positive or negative regulators. This allows for large combinations of potential expression patterns required for complex organisms

Pleiotropic effects

Multiple effects of a single gene on the phenotype of an organism

Operon: a regulatory unit containing

Multiple genes under the control of a single promoter

Primers on the lagging strand

Multiple primers are needed, primase creates primers for both strands

Genetic material variation

Must be capable of change to account for the known phenotypic variation in each species

Genetic material transmission

Must be passed from parent to offspring

Genetic material information

Must encode the information necessary to make an entire organism

Haploinsufficiency (dominant allele)

Mutant is a loss of function allele and one wild type copy is not enough to provide function. Ex: poludactyly in humans

Complementation

Mutant phenotype of parents generation can be returned to WT phenotype in offspring's generation because alleles complement each other

Dominant negative mutations (dominant allele)

Mutant protein acts to antagonize normal protein

Xeroderma pigmentosum

Mutated single strand nucleotide excision repair gene, which prevents repair of thymidine dimers.; Dry skin w/ melanoma and other cancers

Transcriptional repressors

Prevent switch from initiation to elongation. Prevents transcription

Thermostable DNA polymerase in PCR

Necessary because PCR involves heating steps that inactivate most DNA polymerases. Taq polymerase

Like bacteria, chromosomes of mitochondria and chloroplasts are found in

Necleoids

Deleting the 6 N-terminal amino acids to remove the acylation sites

Negates plasma membrane localization and also the phenotype

Nucleic acid charge

Negative charge. Run on a gel from negative to positive

lac operon regulation

Negative control mechanism. Uses lac repressor protein, repressor binds to operator region. When bound, blocks RNApol binding to the promoter. Binding of allolactose, inactivated repressor so that it can not bind to the operator

Transcriptional regulation involves the actions of two main types of regulatory proteins

Negative control-repressors that inhibit transcription and positive control-activators that increase transcription

Lac operon operator

Negative regulation when bound b repressor protein

Histone proteins bind to

Negatively charged phosphates along the DNA backbone via electrostatic interactions and hydrogen bonds

The chromosomal DNA in bacteria is

Negatively supercoiled

Why is an individual with blood type O considered a universal donor?

Neither the A nor B antigens are present on type O red blood cells.

Likely effect on protein function in missense mutation

Neutral or inhibitory

Eukaryotic cells have two types of ribosomes

One type is found in the cytoplasm and the other in organelles: mitochondria and chloroplasts

Negative regulation: a repressor bound to the operator

No transcription

Positive regulation: no activator

No transcription

Autopolyploidy

Non disjunction in meiosis or mitosis results in diploid gametes (failure to separate the chromosome)

Once DNA has been cleaved by CRISPR-Cas9, cells immediately activate DNA repair mechanisms to fix the break by two main pathways

Non homologous end joining and homologous recombination

Characteristics of viruses

Non living particles, medically important-cause many diseases, nucleic acid genomes, both prokaryotic and eukaryotic cells are infected, rely on living cells to replicate

A crossover in meiosis is an exchange of genetic material between

Non sister chromatids of homologous chromosomes

With crossing over

Non sister chromatids of homologous chromosomes exchange DNA segments

Intergenic regions

Non transcribed DNA segments between genes. Play roles in gene regulation, replication, DNA folding, and genetic recombination

Amino acids altered in silent mutation

None

Likely effect on protein function in silent mutation

None

Without crossing over, gametes carry parental combinations of chomosomes

Nonrecombinant cells

Mutation that is usually the most damaging

Nonsense mutations

Pleiotropic effects: cystic fibrosis

Normal allele encodes the cystic fibrosis transmembrane conductance regulator (CFTR). Regulates ionic balance by transporting Cl- ions. Mutant does not transport chloride effectively. Thus defects in CFTR can have multiple effects

DNA pol I and III are involved in

Normal replication

Chromosome structure alteration: simple translocations

One way transfer

The Y chromosomes are what promote the male development

Not XX directly to promote female. XXY can be a male

Integration in viral reproduction

Not all viruses integrate into host chromosome. Once integrated, genome is called prohphage. The stage is called the lysogenic cycle

Observed offspring ratios of linkage is

Not as expected (9:3:3:1 in dihybrid cross)

Disease resistance: Heterozygotes have one altered copy of the gene with slightly reduced protein function

Not enough to cause serious side effects, but enough to prevent infections

Heterozygotes have one altered copy of the gene with slightly reduced protein function

Not enough to cause serious side effects, but enough to prevent infections

F2 generation contains seeds with novel combinations

Not found in the parental generation

If glucose is not present and lactose is not present these genes are

Not transcribed

If glucose is present it is used as the energy source for transcriptions and lacZ, Y, and A are

Not transcribed regardless of the presence of lactose

Smaller fragments migrate at faster rate than large fragments in

Nuclear acid electrophoresis

Genome differences between viruses

Nucleic acids of a virus are the viral genome

Recombination frequency

Number of recombination/total number of offspring x100

Probability is calculated by

Number of times an outcome will occur/total number of possible outcomes

The lac operon has three operator sites for the lac repressor

O1, O2, O3

Globin gene paralogs characteristics correspond to

O2 needs of embryo, fetus, and adult

Homologous recombination repair

Occurs at the double stranded breaks or when DNA damage causes a gap in synthesis during DNA replication. The strands of a normal sister chromatid are used to repair a damaged sister chromatid

A double crossover separates the gene in the middle from the other two genes at either end

Occurs least because it requires two crossover events. Tell us which gene is in the middle

Autoploidy

Occurs when a diploid plant produces diploid gametes due to nondisjunction during meiosis. Results in one diploid cell and one without chromosomes

Phenotypes controlled by imprinted genes have a non mendelian pattern of inheritance

Offspring express either the maternally inherited or the paternally inherited allele but not both (monoallelic expression)

siRNAs don't go through processing events that occur in the nucleus

Pre-siRNA is formed from two RNA molecules that base pair together

Amino acids altered in missense mutation

One

Human individuals that are not 46 (XY) or 46 (XX) still only have

One active X chromosome

Loss of function alleles may have no effect on phenotype

One gene compensates for the loss of another

Pleiotropic effects

One gene has two or more phenotypic effects

When the two factors of a single character are different

One is dominant and its effect can be seen. The other is recessive and is not expressed

In eukaryotes, SRP is composed of

One nc RNA and six different proteins

In bacteria, SRP is composed of

One ncRNA and one protein

Independent assortment

One of Mendel's principles that states that genes for different traits can segregate independently during the formation of gametes

Conditional mutation

One that affects the phenotype only under specific conditions

PIWI interacting RNAs (piRNAs) associate with a class of proteins called

PIWI proteins

Gap genes activate

Pair rule genes that divide emryo into segments

Gap proteins encode other transcription factors that activate

Pair rule genes whose products divide the embryo into smaller regions about two segments wide

In vertebrate there are 4 clusters of hox genes and their order

Parallels the order of body parts in which they are expressed

Homologous genes within a single species are said to be

Paralogs

In normal individuals, trinucleotide sequences are transmitted from

Parent to offspring without mutation

Dispersive model of DNA replication

Parental and daughter DNA are interspersed in both strands following replication

P generation

Parental generation, the first two individuals that mate in a genetic cross

If the offspring of crosses involved linked genes

Parental phenotypes occur most frequently, double crossover phenotypes occur least, single crossover phontypes occur intermediate

Conserved model of DNA replication

Parental strands stay together after DNA replication

Translocation

Part of a chromosome becomes attached to a non homologous chromosome (simple-one way, reciprocal-two way)

Intron RNA is defined by

Particular sequences within the intron and at the into-exon boundaries

Long term maintenance of the change in gene expression

Passed from cell to cell. May be passed from generation to generation

Spacers in modern bacteria are from

Past infections. The spacer is passed to daughter cells

Nonsense mutations result in

Premature termination of translation

Amino acids are bound together by

Peptide bonds in the backbone

Ribosomes contain three discrete sites

Peptidyl site (P site), aminoacyl site (A site), exit site (E site)

Effects of antisense RNA often

Persisted for a very long time in the cell

RNA interference (RNAi)

Phenomenon in which double stranded RNA causes the silencing of mRNA

Unbalanced translocations are associated with

Phenotypic abnormalities or even lethality

Restriction enzymes break

Phosphodiester bonds in the DNA backbone

Main function of chloroplasts

Photosynthesis

Synteny

Physical linkage of genes into the same chromosome

Deletion

Piece of chromosome deleted

Duplications

Piece of chromosome doubled

Inversion

Piece of chromosome flipped

Translocations

Piece of chromosome moved

Recombination between homologous chromosomes in meiosis exchanges

Pieces of the chromosome

In Mirabilis jalapa, leaves can be green white or variegated

Pigmentation is controlled by the chloroplast (the mothers traits)

True breeding lines

Plants that always produce progeny with the same traits with self fertilized (or bred to the same strain)

Benefits of RNA interference

Presents a newly identified form of gene regulation. May offer a defense mechanism against certain viruses. May play a role in silencing certain transposable elements

Episomes

Plasmids that can integrate into the chromosome

RNA can form stem loop structure which may bind to

Pockets on the surface of proteins

No cytoplasm is transferred through

Pollen (male)

Cross fertilization

Pollen and egg are derived from different plants

Self fertilization

Pollen and egg are derived from the same plant

If the polyA tail is too short,

PolyA binding protein can no longer bind. mRNA will rapidly degrade

Isoelectric focusing (IEF) electrophoresis

Polyacrylamide gel with pH gradient. Not denatured protein. Protein separate based on isoelectric point: the pH at which their charge=0

The second strand of cDNA uses

Polymerase I (does the same job in replication

Extension (synthesis) in PCR

Polymerase copies the target sequences

Some proteins are composed of more than one polypeptide

Polypeptide dentores structure and protein denotes function

Lac operon CAP site

Positive regulation site for catabolite activator protein (CAP)

Topoisomerase II alleviates

Positive supercoiling

microRNAs and siRNAs are involved in

Post transcriptional gene silencing and RNA interference

CRISPR-Cas9 uses relatively long recognition sequence (but not 100% specific)

Potentially allows edits anywhere in a genome. Still needs some screening

In eukaryotes, transcription of structural genes, produces a long transcript known as

Pre-mRNA. Requires a splicesosome to remove introns

Western blotting steps

Proteins are extracted from the cell, separated by 1D or 2D PAGE, dissolved in the detergent SDS which denatures proteins and coats them with negative charges. The negatively charged proteins are then separated by polyacrylamide electrophoresis

Initiation of replication in bacteria DnaA

Proteins bind to sequences in oriC (the DnaA box), then additional DnaA proteins bind to the first set

Methylation results in

Proteins binding to the methylated cytosine and inhibiting transcription. A chromatin structure that silences gene expression

Cellular level

Proteins function within the structures of the cell

Quaternary structure of a protein

Proteins made up of two or more polypeptides have a quaternary structure

Antibodies

Proteins that are used in the immune system

Trans acting factors

Proteins that bind to the cis element DNA sequences

Transcription factors

Proteins that influence the ability of RNA polymerase to transcribe a given gene

Methyl-CpG-binding proteins

Proteins which bind methylated sequences

Examples of antigens

Proteins, carbs, nucleic acids, bacteria, viruses, or cells not normally found in the body

Group I and II self splicing can occur in vitro without

Proteins. However, in vivo, proteins known as maturases often enhance the rate of splicing

CRISPR RNAs can combine with Cas proteins to

Provide defense against invasion of specific DNA molecules

First step of gene cloning

Purify designed DNA and vector (plasmid), difest both with a restriction endonuclease

A transition is a change of

Pyrimidine (C, T) to another pyrimidine or a purine (A, G) to another purine

What makes a good model organism

Quick reproduction, large number of organisms, small genome size

Two main classes of drugs inhibit gyrase and other bacterial topoisomerases, but do not inhibit eukaryotic ones

Quinolones and coumarins

Resistance factors

R factors, give resistance to antibiotics

Bacteria have three release factors

RF1, RF2, RF3

DNA serves as the template for the synthesis of

RNA

RNA may be the final product of the gene or

RNA can be translated into a polypeptide

Torpedo model

RNA cut near polyA signal sequence. Polymerase continues until an exonuclease causes complex disassociation

RT PCR

RNA is exposed to reverse transcriptase and made into DNA and that is run through PCR to understand the gene expression

RT-PCR is carried out in the following manner

RNA is made into first strand cDNA. Single-stranded cDNA is used as template DNA in conventional PCR

If we wanted to look at gene expression

RNA isolation, reverse transcription that convert RNA to cDNA. DNA pol synthesizes 2nd cDNA to create the double stranded cDNA

Self splicing does not require enzymes

RNA itself functions as its own ribozyme

Non coding RNAs

RNA made that doesn't encode polypeptide

RNAi (interference)

RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules. Transgene silencing and virus resistance

Ribozyme

RNA molecules with a catalytic function. RNA molecules that have the ability to catalyze a reaction

RNA is electrophoresed, transferred to membrane, then hybridized with a DNA probe in

RNA northern blotting

Nuclear DNA is transcribed by three different RNA polymerases

RNA pol I, RNA pol II, RNA pol III

Basal transcription apparatus

RNA pol II+the five GTFs

Formation of the 3-4 stem loop causes

RNA pol to terminate transcription at the end of the trpL gene

Most regulatory transcription factors do not bind directly to

RNA polymerase

3 categories of proteins are required for basal transcription to occur at the promoter of structural genes

RNA polymerase II, 5 different proteins called general transcription facorts, all protein complex called mediator

Transcription initiation

RNA polymerase binds to DNA. The promoter functions as a recognition site for transcription factors which enables RNA polymerase to bind to the promoter

Example of recriprocal cross in duchenne DMD

Reciprocal crosses demonstrate X linkage in dogs and humans. X linked genes behave differently in reciprocal crosses

In expression, tracrRNA-crRNA complex binds cas9 protein through

Recognition site in tracrRNA

Some splicing factors enhance the ability of a spliceosome to

Recognize a splice site

Base excision repair

Recognize abnormal base and cleaves bond

Splicing factors modulate the ability of spliceosomes to

Recognize or choose the splice sites

Genetic maps can be made by

Recombination analysis or molecular approaches

Inheritance patterns that deviate from Mendels law are seen when there is gene

Redundancy

Goodness of fit

Refers to how close observed data are to those predicted from a hypothesis

Gene cloning

Refers to isolating, and then making many copies of a particular sequence of DNA

The genome in eukaryotes

Refers to one complete set of nuclear chromosomes

Development in cellular biology

Refers to the process that cells and organs undergo in order to reach their final form

Possible hairpin structures

Region 1 and 2, region 3 and 4, region 2 and 3

Terminator sequence

Region in the DNA where RNA synthesis stops

Operon allow bacteria to

Regulate a group of genes that encode for proteins involved in a common process

MADS-Box genes

Regulate large processes. Homeodomains that when active transcribe proteins to start cascade

Transcription factors-DNA binding domain allows the HOX protein to the DNA to

Regulate transcription of a given gene

Gene expression can be

Regulated or unregualted

miRNAs play key roles in

Regulating gene expression, especially during development

microRNAs

Regulation of gene expression

Imprinting control regions (ICRs)

Regulatory elements near imprinted genes that contain transcription factor binding sites (cis acting). Methylated either in the oocyte or sperm but not both

For protein encoding genes 3 features are found in most promoters

Regulatory elements, TATA box, transcriptional start site

Example of sex limited traits: bird plumage and features

Roosters have more ornate plumage than hens, and larger comb and wattles

In humans unique or non repetitive DNA sequeces make up

Roughly 41% of the genome

Polytene chromosomes occur mainly in

Salivary glands of drosophila and a few other insects

Replica plating

Same bacterial cells can be transferred to two plates at the same time. Measure number of tonr resistant colonies-cells resistant to T1 bacteriophage

Probe in northern blot

Same steps as southern blot but replace DNA with RNA and replace some reagents.Detection of specific RNA sequence

RNA polymerase holoenzyme binds loosely to the DNA in bacteria

Scans along the DNA until promoter is reached. Sigma factor recognizes the -35 and -10 regions. Sigma factor that contains a helix trun helix motif gives tighter binding to the DNA

Cytogeneticist

Scientist who studies chromosomes under the microscope

Non research applications of PCR

Screening for mutations involved in genetic disorders. Diagnostic detection of bacteria and viruses in humans and pathogens. Advantageous when studying samples from single cells

Intragenic suppressor

Second mutation in the same gene as the first

Intergenic suppressor

Second mutation is in a different gene than the first

Although sterility is generally a detrimental trait it can be agriculturally desirable

Seedless fruit (triploid varieties propagated by cuttings), seedless flowers (triploid varieties keep blooming longer)

Pangenesis

Seeds produced by all parts of body, collected and transmitted to offspring at conception

Chromosome structure alteration: translocation

Segment of one chromosome becomes attached to a non-homologous chromosome

Pair rule genes control transcription of

Segment polarity genes

Positional information laid down by molecular gradients is interpreted by two sets of zygotic (embryonic genes)

Segmentation genes and homeotic selector

HOX genes are conserved across

Segmented eukaryotes

Transposable elements

Segments of DNA that can become integrated into chromosomes

Physiological adaptation hypothesis

Selected conditions promote formation of specific mutations allowing the organism to survive

Mendel carried out two types of crosses

Self fertilization and cross fertilization

Group I and group II introns are removed by

Self splicing

Signaling systems in early embryonic development act both independtly and in coordinated networks to

Send and receive developmental signals that elicit specific transcriptional responses

Flowers are made of 4 concentric whorls

Sepals, petals, stamens, carpels

PFGE gel electrophoresis

Separation based on re orientation time of DNA strands. Can separate up to 2Mb

Regulatory transcription factors recognize

Sequence elements located near the core promoter. These sequences are known as control or regulatory elements

A translational regulatory protein recognizes

Sequences within the mRNA

Recombinant analysis

Series of crosses specifically aimed at identifying the position of different genes based on the principle of recombination

piRNA genes are usually organized into clusters in which a single pre-piRNA transcript contains

Several different piRNA sequences

Selection is critical for two main reasons

Several different types of product come out of a DNA ligation and a very low percentage of E.coli transformed with plasmid in during transformation

The stability of eukaryotic mRNA varies considerably

Several minutes to several days

Anticipation or dynamic mutation

Severity of disease tends to worsen in future generations

Two unusual features of TRNE disorders

Severity of disease tends to worsen in future generations and severity depends on whether it's inherited from the mother or father

Dynamic mutation

Severity of disease worsens in future generations

In many species, sex determination relies on

Sex chromosomes that are different in males and females. Other mechanisms are environmental or behavioral interactions

Traits that occur in only one of the two sexes

Sex limited traits

A punnett square can be used to predict the outcome of mating if a gene is

Sex linked

Sex affects the phenotype of the individual; some alleles are recessive in one sex and dominant in the opposite sex

Sex linked inheritance

Different chromosomes of the same species can be distinguished from each other and can be classified by

Size, centromere position, banding pattern

Phenotypic consequences of duplications tend to be correlated with

Size. Likely to have phenotypic effects for large pieces of chromosome

Molecular events of conjugation

Sex pilus contacts F- cell, shortens, and a conjugation bridge is formed between cells. A protein complex called the relaxosome binds the origin of transfer in the F factor DNA, and cuts one strand of the DNA. The relaxosome separates the strands ofDNA, leaving the protein relaxase bound. DNA/relaxase complex is pumped out of the donor cell. After transfer of one strand of the F factor, relaxase rejoins the ends to form a circle

Binding of mRNA to the 30S subunit is facilitated by a ribosomal-binding site or

Shine-dalgarno sequence. Complementary to a sequence in the 16S rRNA

Attenuation

Short transcript produced that is translated into a short peptide called leader peptide

The repeats in Crispr are interspersed with

Short, unique sequences, which are called spacers

As mRNA ages, its polyA tail is

Shortened by the action of cellular exonucleases

Example of missense mutation

Sickle cell amenia

Examples of heterozygotes with an altered copy of the gene for disease resitance

Sickle cell anemia and malaria, and tay sachs disease: heterozygotes resistant to tuberculosis

Example of over dominance

Sickle cell anemia. Autosomal recessive disorder where abnormal hemoglobin is produced. Two alleles HbA encodes normal hemoglobin (A) and HbS encodes abnormal hemoglobin (S)

Initiation in bacteria

Sigma factor is needed for promoter recognition

Notch encodes a transmembrane signal receptor

Signal is the delta transmembrane protein. Activates transcription to controls specific developmental pathways

Homologous recombination

Similar DNA segments break and rejoin to form new combinations during crossing over in meiosis

Mismatch repair

Similar to excision repair except that the DNA defect is a base pair mismatch in the DNA not an abnormal DNA

Inheritance of phenotypes follow mendels laws

Simple mendelian inheritance

Mutations may occur at the chromosomal or

Single gene level

What keeps the parental strands apart?

Single strand binding proteins

tRNAs contain both

Single stranded and double stranded regions

RNA is usually

Single stranded but can be double stranded

Polyribosomes or polysomes

Single transcripts that multiple ribosomes are translating simultaneously

dd snail mothers produce

Sinistral offspring even if the offspring are Dd

Crossing over between sister chromatids does not produce a new combination of alleles

Sister chromatids are genetically identical

mRNA ribosome binding site

Site for ribosome binding; translation begins near this site in mRNA

DNA regulatory sequences

Site for the binding of regulatory proteins is to influence the rate of transcription

Promoter sequence

Site in the DNA where the enzymes that synthesize RNA will first bind

Regulatory sequence

Sites in the DNA where proteins interact to control transcription

Structural differences between viruses

Size and shape of the capsid (protein coat) and presence or absence of viral envelope

Phenotypic consequences of deletions depends on

Size of deletion and chromosomal material deleted

Chromosomes are classified by

Size, centromere position and banding pattern

If mirabili jalapa plant develops from a zygote with both mutant and wild type chloroplasts

Some cells get all wild type, some get all mutant, and some get a mix

A gene normally in two copies in a diploid cell may be found in 1, 3, or more copies

Some chromosomes are missing the gene, some have extra copies (segmental duplication)

Often, large sections of the coding region are the same, resulting in two alternative versions of a protein that have similar functions

Some exons always used-constitutive exons, some are not-alternative exons

Dosage compensation mechanisms vary for different species

Some have increased expression in heterogametics and some have decreased expression in homogametics

A forward mutation changes the wild type genotype into

Some new variation

Crossing over results in

Some of the gametes carrying new combinations of alleles - genetic recombination (recombinant cells)

Homodimer formation in overdominance

Some proteins function as homodimers-composed of two subunits

Exon skipping

Some splicing factors inhibit the ability of a splicesome to recognize a splice site

Duplications and mutations have created many histone variants

Some variants play specialized roles in chromatin structure and function

siRNAs play a key role in

Some viral infections. Also useful experimental tools

Heterochromatic effect

Something flipped or moved to a region that's caused it to be heterochromatic

Chromosomal DNA fragments

Source of the DNA segment of interest. DNA purified using a variety of biochemical techniques from tissues and cell of interest

Blots that use hybridization

Southern and northern, not western

Specification in development

Spatially distinct differences in cell types (still reversible)

Telomeres

Special DNA repeat sequences at the ends of the DNA with associated proteins

Splice junctions

Spliceosome may not recognize splice site-intron is included when it shouldn't be

Self splicing

Splicing among group I and II introns

Spliceosome mechanism

Splicing in this case requires a multicomponent structure known as the spliceosome

Insertion of P elements into intron can affect

Splicing or cause premature termination of transcription

After transcription, RNA is modified in eukaryotes

Splicing, capping, poly-A addition tail

Tn elements can move from plasmids onto bacterial chromosomes

Spreading multiple drug resistance between different bacterial strains

Poly-A addition tails are added at the 3' end of RNA for

Stability

PolyA binding protein binds to the polyA tail and enhances

Stability

Depending on the restriction enzyme used, DNA can be cleaved in two different ways

Staggered ends or blunt ends

AUG codon

Start codon (all polypeptides start with this)

To measure the norm of reaction

Start with a true breeding strain of animals with the same genotype, and subject them to different environmental conditions

Termination in transcription

Stem loop

Cleaved end that is more efficient for ligation reactions

Sticky ends/staggered ends

Enhancers

Stimulate transcription

The function of genetic material is to

Store information required to produce an organism. The DNA molecule does so through its base sequence

Z, Y, and A are component of the lac operon that are

Structural

Protein encoding genes

Structural genes. Account for the majority of bacterial DNA

Copy number variation

Structural variation where a DNA segment 1000bp or larger has copy number differences in members of a species

ncRNAs can bind to different types of molecules by

Structurally changing like making loops

Model organisms can be used to

Study human embryonic development and associated genetic disorders

Gap genes are activated to

Subdivide embryo intro broad bands

Hybrid dysgenesis

Sudden appearance of numerous mutations, chromosome aberrations, and sterility in the offspring of a cross between a male fly that possesses P elements and a female fly that lacks them

Intragenic suppressor mutation

Suppresses the effect of an earlier mutation within the same gene. Second mutation in the same gene as the first

Competence factors

Surface proteins that allow a bacterium to take up DNA in transformation

Example of behavioral sex determination in clownfish

Switch from male to female. Male and female clownfish have the same chromosome composition

In homeotic mutants, the structure formed by one segment is

Switched to that of a neighboring segment

Transcriptional activators stimulate mediator

Switching from initiation to elongation

The code is degenerate

Synonymous codons specify the same amino acid. (GGU, GGC, GGA, GGG all code for glycine)

Mutations in HOXD13 cause

Synpolydactyly (SPD), characterized by extra fingers and toes and abnormalities in bones of the hands and feet

Bidirectional

Synthesis occurs in both directions in bacterial chromosomes. Two replication forls move in opposite direction from one origin of replication

DNA sequences are necessary for

Synthesis of RNA and cellular proteins, replication of chromosomes, proper segregation of chromosomes, compaction of chromosomes

Nucleotide sequence of the target DNA must be known in order to

Synthesize primers in PCR

Helper T cells

T cells that help the immune system by increasing the activity of killer cells and stimulating the suppressor T cells

Examples of cis acting elements

TATA box, enhancers and silencers

ncRNA that facilitates the binding of telomerase to the telomere and acts as a template for DNA replication

TERC

Selfish DNA hypothesis

TEs exist because they can. Like parasite, they proliferate in hosts as long as they don't overly harm the hosts

CTD phosphorylation breaks the contact between

TFIIB and RNA polymerase II

Some prokaryotes have a system that defends against foreign invaders

The CRISPR-Cas system. Defense against bacteriphages, plasmids, and transposons. ncRNAs play a key role in determining what is being targeted

If sanger sequencing is used to stop at each base

The DNA can be built back together

Primosome is physcially associated with

The DNA polymerase holoenzyme forming the replisome

Coding strand is the same sequence as

The RNA

The pre-piRNA is processed into one or more piRNAs and each piRNA is complementary to

The RNA of a particular transposable element

Most common type of chromosomal rearrangement in humans

The Robertsonian translocation. Majority of chromosome 21 is attached to 14

A 17 base pair open complex is formed when

The TATA box in the -10 region is unwound. A short RNA strand is made within the open complex and the sigma factor is released, marking the end of initiation

Transcriptional start site

The TATA box plus transcritpional start site comprise the core promoter

The X inactivation center contains

The X inactive specific transcript gene

Bacteria lack nuclei so both transcription and transolation occur in

The cytoplasm

If mitotic recombination occurs during an early stage of embryonic development

The daughter cells containing the recombinant chromosomes continue to divide. May result in a patch of tissue with characteristics that are different than the rest of the organism

In mice, runt is expressed in

The development and formation of blood cells, bone, and the genital system

Interactions between sets of genes results in

The development of specific organs

The percentage of recombinant offspring is correlated with

The distance between the two genes

Telomeres solves the problem of

The ends of linear chromosomes becoming shorter after each DNA replication

Inheritance patterns that deviate from Mendels law are seen when phenotype is influenced by

The environment

Explanation for the cause of incomplete penetrance and variable expressivity

The environment may affect the outcome of the trait and there may be modifier genes that affect the phenotype, which differ in different individuals

Thymine dimers are repaired by

The enzyme DNA photolyase, exposure to light, and transfer of an electron to the dimer

How often genes independently assort depends on how far apart they are on the chromosome

The more DNA between two genes, the longer the chromosome, the higher the likelihood that there will be crossing over between genes

Wild type allele

The most prevalent version of a gene in wild populations. Wild type proteins function normally. They promote the reproductive success of the organism

In humans, mitochondria are inherited from

The mother

The bacterial chromosome is found in a region of the cell called

The nucleoid. Not surrounded by a membrane, DNA is in direct contact with the cytoplasm

Translation

The nucleotide sequence in RNA provides the information to produce the amino acid sequence of a polypeptide

Chromosomes in eukaryotes are located in

The nucleus

The chromosomes of a eukaryotic cell are found in

The nucleus

Map distance

The number of recombinant offspring divided by the total number of offspring, multiplied by 100

In haplodiploid sex determination the sex is determined by

The number of sets of chromosomes

Sequence complexity

The number of times a particular base sequence appears in the genome

Simple transposition can increase

The number of transposons in genomes

The number of linkage groups equals

The number of types of chromosomes of the species

DNA ligase covalently links

The okazaki fragments together

Nucleoids may contain many copies of

The one chromosome

Loss of gene function changes interactions between set of genes and

The organs fate

The pre-replication complex includes

The origin recognition complex

Sugar phosphate backbone is on

The outside

Phenotype

The outward appearance of an individual

In mice with the Igf-2, imprinting causes expression of

The paternal allele but not the maternal. Paternal allele is transcribed into RNA

The central dogma of genetics

The path from gene to protein to trait

Histone cody hypothesis

The pattern of histone modification acts much like a language or code in specifying alterations in chromatin structure

Gene redundancy

The phenomenon in which an inactive gene is compensated for by another gene with a similar function

Plants and animals diverged from a common unicellular ancestor after

The rise of eukaryotes and before the rise of multicellular organisms

Intergenic suppressor. Polypeptides may be subunits of

The same multimeric protein

Mendels law of segregation can be explained by

The separation of homologous chromosomes during meisosis

The sequence of codons within mRNA determines

The sequence of amino acids within a polypeptide

Termination occurs when

The short RNA-DNA hybrid of the open complex is forced to seperate and the newly made RNA is released

Tertiary structure of a protein

The short regions of secondary structure in a protein fold into a 3D tertiary structure. This is the final conformation of proteins that are composed of a single polypeptide

Insertion elements

The simplest type of transposable element. Both ends have inverted repeats. Also called trasposase gene

Origin of replication

The site of initiation and point of control for whole process

What determines the sex of the zygote

The sperm

Chromosomes

The structures that contain the genetic material. Complexes of DNA and proteins

Epigenetics

The study of mechanisms that lead to changes in gene expression, can be passed from cell to cell, are reversible, and do not change the DNA sequence. Change in gene expression not based on DNA sequence

Catabolite repression

The suppression of alternative catabolic pathways by a preferred source of carbon and energy

Because ncRNAs are made of nucleic acids

They can be targeted to different places in the genome or into RNAs

When transposon activity is not regulated and kept under control

They can cause chromosomal abnormalities and sterility

Only certain strains of bacteria can act as donor cells in conjugation

They contain a small circular DNA called an F factor (fertility factor)

Transposable elements are complete (autonomous) when

They contain all the information necessary for transposition to occur

How does UV light and other nonionizing radiation damage DNA molecules?

They create thymine dimers between adjacent thymines in the DNA chain

Transposable elements are incomplete (nonautonomous) when

They lack a gene that is necessary for transposition to occur

Advantages of using pea plants for genetics

They're small and easily grown. Each flower has male and female structures. Many different varieties were available with different traits

Heterochromatin

Tightly compacte regions of chromosomes, transcriptionaly inactive, radial loop domains compacted even further

Nonessential genes

Those not required for survival, but nonessential genes can form lethal alleles

Y linked or holandric genes

Those on Y only. Transmitted from fathers to sons

Four values means

Three degrees of freedom

RNA polymerase in eukaryotes

Three types of RNA polymerases; RNA polymerase II transcribes protein encoding genes

Maintenance in X inactivation

Through mitosis and beyond

Nucleotide excision repair can repair many types of DNA damage including

Thymine dimers and chemically modified bases, and missing bases

Determination in development

Time point at which a specific developmental fate is fixed (irreversible)

Determination

Time point when a specific developmental fate becomes fixed

CpG islands tend to be methylated in

Tissue specific genes when they are not expressed

DNA polymerase function

To add to the growing strand, DNA polymerase uses a dNTP (3 phosphate groups attached at the 5' C)

Purpose of genetic mapping

To determine the linear order of linked genes along the same chromosome. Helps identify genes regulating things we don't know about

Why eukaryotes have multiple origins of replication

To ensure that DNA can be replicated in a reasonable time

SNOW DROP

To remember the types of blotting

Ames test used to evaluate mutagenicity

To see if an agent increases the reversion rate. Uses a strain of salmonella that cannot synthesize the amino acid histidine. Has point mutation in a gene involved in histidine synthesis

mtDNA analysis is a main tool in

Tracking human evolution and migrations

Sex limited

Traits occurs in only one of the two sexes resulting in sexual dimorphism. May be autosomal or sex linked

Organism level

Traits seen at the organism level arise from molecular and cellular properties

Expression in CRISPR-Cas

Transcribed into a long precursor RNA. Cleaved by Cas proteins and processed into crRNAs, each having one spacer sequence. crRNA combined with Cas protein to form an effector complex

If glucose is not present and lactose is present these genes are

Transcribed. Lactose induces the transcription of the lacZ, Y, and A genes

RNA polymerase III in eukaryote transcription

Transcribes all genes for tRNAs

RNA polymerase I in eukaryote transcription

Transcribes all of the genes for ribosomal RNAs

RNA pol III

Transcribes all tRNA genes and the 5S rRNA gene

Gene expression occurs in two steps

Transcription and translation

Molecular level

Transcription and translation produce proteins

Genetic regulation in bacteria is exercised predominantly at the level of

Transcription but there are many examples of regulation that occurs at a later stage in gene expression

Closed conformation of chromatin

Transcription does not take place

Gap proteins

Transcription factors that activate specific pair rule genes. Further division of embryo

Transitions are more common than

Transversions

RNA pol I

Trascribes al rRNA genes (except 5S rRNA)

Crossing of the tetraploid to the original diploid plants will result in

Triploid (3n) offspring which are sterile (impaired meiosis)

The chromosomal anomaly that happens in down syndrome is classified as

Trisomy

When trytophan levels are high

Trytophan acts as a corepressor that binds the trp repressor protein. The trytophan trp repressor complex then binds the the operator site to inhibit transcription

Virulence plasmids

Turn the bacterium into a pathogenic strain

Polyploids (three or more sets of chromosomes) are sterile unless the number is divisible by

Two

At the molecular level, over dominance is due to

Two alleles that produce slightly different proteins

Example of conditional mutation: temperature sensitive (ts) mutants

Used by geneticists to study gene function. E. coli with a ts mutant may grow below 38 degrees but not above 40 degrees

Mendels work was novel

Used quantitative analysis. Developed general laws to predict which phenotypes would appear in offspring and ratios of phenotypes in the offspring

Western (protein) blotting

Used to identify a specific protein within a protein mixture (separated by PAGE)

Fluorescent in situ hybridization (FISH)

Used to identify the location (on a chromosome) of a DNA or RNA of interest

Gene cloning produces an enormous amount of a single DNA sequence

Useful for study and further manipulation

Dideoxy (sanger) method

Uses DNA polymerase to copy a strand of DNA. DNA synthesis is terminated at specific nucleotides by adding dideoxyribonucleotides (ddNTPs) to the reaction. These can be added to a growing polynucleotide chain, but no new nucleotides can be added

Nucleic acid electrophoresis

Uses an electric field to separate DNA and/or RNA fragments by size

Genetic knock down studies

Uses the natural RNAi system. Construct DNA sequence complementary to gene of interest that form a hair pin structure. Leads to double stranded RNA, activation of Dicer and RISC systems

Allopolyploidy begins when two species hybridize

Usually results in a sterile hybrid as the haploid sets cannot pair properly at meiosis

Gene mutation

Usually single base point changes that change one nucleotide to another. Not detectable by karyotype bc too small. Deletion or insertion of nucleotides

Attachment in virual reproduction

Usually specific or only a few cells. Proteins on the virus interact with specific molecules at the cell surface

In E. coli, the NER system requires four key proteins

UvrA, UvrBm UvrC, and UvrD. Named because they are involved in ultraviolet light repair of pyrmidine dimers. Also important in repairing chemically damaged DNA

What protein cuts the damaged DNA strand?

UvrC

Histone cenH3

Variant the is found only at the centromere

Euploidy

Variation in the number of complete sets of chromosomes. Changes the ploidy level. Generally nonviable in animals but important for evolution in plants

Euploidy

Variation in the number of complete sets of chromosomes. Occur occasionally in animals but frequently in plants. Ex: triploid (3n) and tetraploid (4n)

Genomic imprinting: expression of a gene depends on

Whether it is inherited from the male or female parent. Several mammalian genes are imprinted

Mismatch repair system uses methylation patterns to identify

Which base was incorrectly paired (if this system is broken, we see cancer)

trpL RNA can form three different hairpin structures

Which form depends on speed of translation of the leader peptide

Gene cloning is used for

Whole genes or parts of genes

RNAi provides a defense against viruses

Widely used by plants to prevent viral infections

A gene with multiple alleles may have two or more

Wild types

Calico cats exhibit

X chromosome inactivation

Examples of epigenetic inheritance

X chromosome inactivation and genomic imprinting

Initiation in X inactivation

X chromosome is selected fro inactivation

A male is hemizygous for

X linked genes. Since there is only one copy

Inheritance of genes that are located on the X chromosome

X linked inheritance

Ionizing radiation

X rays, gamma rays. Deletions, nicks, cross linking

Turner syndrom

X0 no Barr body

How does a steroid hormone exert its effect upon a cell?

binds to an intracellular receptor to form a complex that then acts as a transcription factor

In the presence of glucose, adenylyl cyclase is inhibited

cAMP levels decrease. cAMP is no longer available to bind CAP, transcription rate decreases

cAMP-CAP complex is an example of induciblegenetic regulation under positive ccontrol

cAMP-CAP complex binds to the CAP site near the lac promoter and transcription rate increases

Regulation of the lac operon: negative control of expression

lacI encodes for a repressor protein, repressor binds to operator region, RNA polymerase cannot reach the promoter when the repressor is bound

Gene responsible for producing the protein that converts lactose to allolactose

lacZ

Lac operon protein encoding genes

lacZ, lacY, lacA

rRNA

ribosomal RNA; type of RNA that makes up part of the ribosome in translation

F1 generation

the first generation of offspring obtained from an experimental cross of two organisms

Phage lambda

well-known bacteriophage that has been widely used in genetic studies & is often a vector for DNA libraries